4-56467655-G-C

Position:

chr4-56467655-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_006947.4(SRP72):c.20G>C(p.Gly7Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,561,500 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G7G) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0073 ( 20 hom., cov: 31)

Exomes 𝑓: 0.00073 ( 12 hom. )

Consequence

SRP72
NM_006947.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 2.24

Variant links:

Genes affected

SRP72 (HGNC:11303): (signal recognition particle 72) This gene encodes the 72 kDa subunit of the signal recognition particle (SRP), a ribonucleoprotein complex that mediates the targeting of secretory proteins to the endoplasmic reticulum (ER). The SRP complex consists of a 7S RNA and 6 protein subunits: SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72, that are bound to the 7S RNA as monomers or heterodimers. SRP has at least 3 distinct functions that can be associated with the protein subunits: signal recognition, translational arrest, and ER membrane targeting by interaction with the docking protein. Mutations in this gene are associated with familial bone marrow failure. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]

SRP72 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0066815317).

BP6

Variant 4-56467655-G-C is Benign according to our data. Variant chr4-56467655-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 377137.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0073 (1111/152254) while in subpopulation AFR AF= 0.0255 (1059/41550). AF 95% confidence interval is 0.0242. There are 20 homozygotes in gnomad4. There are 515 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1111 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SRP72	NM_006947.4 linkuse as main transcript	c.20G>C	p.Gly7Ala	missense_variant	1/19	ENST00000642900.1	NP_008878.3
SRP72	NM_001267722.2 linkuse as main transcript	c.20G>C	p.Gly7Ala	missense_variant	1/17		NP_001254651.1
SRP72	XM_024454192.2 linkuse as main transcript	c.20G>C	p.Gly7Ala	missense_variant	1/17		XP_024309960.1
SRP72	NR_151856.2 linkuse as main transcript	n.39G>C		non_coding_transcript_exon_variant	1/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRP72	ENST00000642900.1 linkuse as main transcript	c.20G>C	p.Gly7Ala	missense_variant	1/19		NM_006947.4	ENSP00000495128	P1	O76094-1
SRP72	ENST00000510663.6 linkuse as main transcript	c.20G>C	p.Gly7Ala	missense_variant	1/17	1		ENSP00000424576		O76094-2
SRP72	ENST00000504757.2 linkuse as main transcript	c.20G>C	p.Gly7Ala	missense_variant	1/5	2		ENSP00000473576

Frequencies

GnomAD3 genomes

AF:

0.00729

AC:

1109

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0255

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00209

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000162

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00163

AC:

326

AN:

199632

Hom.:

AF XY:

0.00119

AC XY:

132

AN XY:

110750

show subpopulations

Gnomad AFR exome

AF:

0.0235

Gnomad AMR exome

AF:

0.00182

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000118

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000969

Gnomad OTH exome

AF:

0.00113

GnomAD4 exome

AF:

0.000731

AC:

1030

AN:

1409246

Hom.:

Cov.:

AF XY:

0.000650

AC XY:

455

AN XY:

699876

show subpopulations

Gnomad4 AFR exome

AF:

0.0247

Gnomad4 AMR exome

AF:

0.00209

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000290

Gnomad4 SAS exome

AF:

0.000173

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000975

Gnomad4 OTH exome

AF:

0.00164

GnomAD4 genome

AF:

0.00730

AC:

1111

AN:

152254

Hom.:

Cov.:

AF XY:

0.00692

AC XY:

515

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0255

Gnomad4 AMR

AF:

0.00209

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000162

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.000468

Hom.:

Bravo

AF:

0.00873

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.0173

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00216

AC:

262

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:5

Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The SRP72 p.Gly7Ala variant was not identified in the literature or in the Cosmic database but was identified in dbSNP (ID: rs139502866), ClinVar (reported benign and likely benign) and LOVD 3.0. The variant was identified in control databases in 547 of 230982 chromosomes (8 homozygous) at a frequency of 0.002368 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 481 of 19916 chromosomes (freq: 0.02415), Latino in 46 of 25576 chromosomes (freq: 0.001799), Other in 6 of 5494 chromosomes (freq: 0.001092), South Asian in 3 of 25530 chromosomes (freq: 0.000118), European (non-Finnish) in 11 of 108258 chromosomes (freq: 0.000102), but was not observed in the Ashkenazi Jewish, East Asian, and European (Finnish) populations. The p.Gly7 residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, and BLOSUM) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Feb 08, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 08, 2021	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jan 09, 2017

- -

Autosomal dominant aplasia and myelodysplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.016

T;.;T;T

Eigen

Benign

-0.15

Eigen_PC

Benign

-0.10

FATHMM_MKL

Benign

0.70

LIST_S2

Benign

0.73

T;T;.;T

MetaRNN

Benign

0.0067

T;T;T;T

MetaSVM

Benign

-0.33

MutationAssessor

Benign

1.2

L;L;L;.

MutationTaster

Benign

0.98

D;D

PrimateAI

Benign

0.45

PROVEAN

Benign

-0.59

N;N;.;.

REVEL

Benign

0.27

Sift

Benign

0.31

T;T;.;.

Sift4G

Benign

0.55

T;T;.;T

Polyphen

0.060

B;.;B;.

Vest4

0.070

MVP

0.77

MPC

0.32

ClinPred

0.048

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.050

gMVP

0.27

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over