4-56467654-G-T

Position:

chr4-56467654-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006947.4(SRP72):c.19G>T(p.Gly7Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00179 in 1,556,654 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G7G) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0027 ( 11 hom., cov: 31)

Exomes 𝑓: 0.0017 ( 49 hom. )

Consequence

SRP72
NM_006947.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 4.46

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=0.0047951043).

BP6

Variant 4-56467654-G-T is Benign according to our data. Variant chr4-56467654-G-T is described in ClinVar as [Benign]. Clinvar id is 349112.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SRP72	NM_006947.4 linkuse as main transcript	c.19G>T	p.Gly7Trp	missense_variant	1/19	ENST00000642900.1	NP_008878.3
SRP72	NM_001267722.2 linkuse as main transcript	c.19G>T	p.Gly7Trp	missense_variant	1/17		NP_001254651.1
SRP72	XM_024454192.2 linkuse as main transcript	c.19G>T	p.Gly7Trp	missense_variant	1/17		XP_024309960.1
SRP72	NR_151856.2 linkuse as main transcript	n.38G>T		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.19G>T	p.Gly7Trp	missense_variant	1/19		NM_006947.4	ENSP00000495128	P1	O76094-1
SRP72	ENST00000510663.6 linkuse as main transcript	c.19G>T	p.Gly7Trp	missense_variant	1/17	1		ENSP00000424576		O76094-2
SRP72	ENST00000504757.2 linkuse as main transcript	c.19G>T	p.Gly7Trp	missense_variant	1/5	2		ENSP00000473576

Frequencies

GnomAD3 genomes

AF:

0.00270

AC:

411

AN:

152090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000916

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.0626

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000118

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00489

AC:

965

AN:

197496

Hom.:

AF XY:

0.00429

AC XY:

470

AN XY:

109684

show subpopulations

Gnomad AFR exome

AF:

0.000722

Gnomad AMR exome

AF:

0.000246

Gnomad ASJ exome

AF:

0.00694

Gnomad EAS exome

AF:

0.0718

Gnomad SAS exome

AF:

0.000829

Gnomad FIN exome

AF:

0.0000485

Gnomad NFE exome

AF:

0.000109

Gnomad OTH exome

AF:

0.00254

GnomAD4 exome

AF:

0.00169

AC:

2368

AN:

1404446

Hom.:

Cov.:

AF XY:

0.00162

AC XY:

1127

AN XY:

697194

show subpopulations

Gnomad4 AFR exome

AF:

0.000336

Gnomad4 AMR exome

AF:

0.000281

Gnomad4 ASJ exome

AF:

0.00760

Gnomad4 EAS exome

AF:

0.0512

Gnomad4 SAS exome

AF:

0.000960

Gnomad4 FIN exome

AF:

0.0000191

Gnomad4 NFE exome

AF:

0.0000747

Gnomad4 OTH exome

AF:

0.00424

GnomAD4 genome

AF:

0.00271

AC:

413

AN:

152208

Hom.:

Cov.:

AF XY:

0.00297

AC XY:

221

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.000915

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.0630

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000118

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00124

Hom.:

Bravo

AF:

0.00342

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00

AC:

ExAC

AF:

0.00561

AC:

679

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 15, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -

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

Pathogenic

0.65

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.11

CADD

Pathogenic

DANN

Uncertain

0.99

DEOGEN2

Benign

0.051

T;.;T;T

Eigen

Uncertain

0.42

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.83

T;T;.;T

MetaRNN

Benign

0.0048

T;T;T;T

MetaSVM

Benign

-0.42

MutationAssessor

Uncertain

2.1

M;M;M;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-2.1

N;N;.;.

REVEL

Uncertain

0.51

Sift

Uncertain

0.0070

D;D;.;.

Sift4G

Uncertain

0.011

D;D;.;D

Polyphen

0.98

D;.;D;.

Vest4

0.36

MVP

0.90

MPC

0.89

ClinPred

0.034

GERP RS

4.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.6

Varity_R

0.12

gMVP

0.34

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