Variant 3-156548985-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_007107.5(SSR3):c.279G>A(p.Glu93Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,612,430 control chromosomes in the GnomAD database, including 15,127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1554 hom., cov: 33)

Exomes 𝑓: 0.13 ( 13573 hom. )

Consequence

SSR3
NM_007107.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.885

Variant links:

Genes affected

SSR3 (HGNC:11325): (signal sequence receptor subunit 3) The signal sequence receptor (SSR) is a glycosylated endoplasmic reticulum (ER) membrane receptor associated with protein translocation across the ER membrane. The SSR is comprised of four membrane proteins/subunits: alpha, beta, gamma, and delta. The first two are glycosylated subunits and the latter two are non-glycosylated subunits. This gene encodes the gamma subunit, which is predicted to span the membrane four times. [provided by RefSeq, Aug 2010]

SSR3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 3-156548985-C-T is Benign according to our data. Variant chr3-156548985-C-T is described in ClinVar as [Benign]. Clinvar id is 1537157.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.885 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSR3	NM_007107.5 link	c.279G>A	p.Glu93Glu	synonymous_variant	3/5	ENST00000265044.7	NP_009038.1	Q9UNL2-1
SSR3	NM_001308197.2 link	c.279G>A	p.Glu93Glu	synonymous_variant	3/5		NP_001295126.1	Q9UNL2-2
SSR3	NM_001308204.2 link	c.123G>A	p.Glu41Glu	synonymous_variant	3/5		NP_001295133.1	Q9UNL2C9J365
SSR3	NM_001308205.2 link	c.123G>A	p.Glu41Glu	synonymous_variant	3/5		NP_001295134.1	Q9UNL2C9J365

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSR3	ENST00000265044.7 link	c.279G>A	p.Glu93Glu	synonymous_variant	3/5	1	NM_007107.5	ENSP00000265044.2		Q9UNL2-1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21269

AN:

151996

Hom.:

1540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.0877

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.151

GnomAD3 exomes

AF:

0.146

AC:

36555

AN:

250206

Hom.:

2871

AF XY:

0.147

AC XY:

19841

AN XY:

135360

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.160

Gnomad ASJ exome

AF:

0.0901

Gnomad EAS exome

AF:

0.200

Gnomad SAS exome

AF:

0.181

Gnomad FIN exome

AF:

0.135

Gnomad NFE exome

AF:

0.132

Gnomad OTH exome

AF:

0.134

GnomAD4 exome

AF:

0.133

AC:

194146

AN:

1460314

Hom.:

13573

Cov.:

AF XY:

0.134

AC XY:

97253

AN XY:

726516

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.161

Gnomad4 ASJ exome

AF:

0.0879

Gnomad4 EAS exome

AF:

0.200

Gnomad4 SAS exome

AF:

0.175

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.140

AC:

21315

AN:

152116

Hom.:

1554

Cov.:

AF XY:

0.141

AC XY:

10494

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.142

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.0877

Gnomad4 EAS

AF:

0.214

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.142

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.128

Hom.:

737

Bravo

AF:

0.138

Asia WGS

AF:

0.239

AC:

828

AN:

3478

EpiCase

AF:

0.130

EpiControl

AF:

0.130

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 02, 2025	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

9.6

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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