Variant 3-156548976-A-G 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.288T>C(p.Val96Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 1,613,316 control chromosomes in the GnomAD database, including 396 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 54 hom., cov: 33)

Exomes 𝑓: 0.0062 ( 342 hom. )

Consequence

SSR3
NM_007107.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.20

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=-0.44).

BP6

Variant 3-156548976-A-G is Benign according to our data. Variant chr3-156548976-A-G is described in ClinVar as [Benign]. Clinvar id is 1632898.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSR3	NM_007107.5 link	c.288T>C	p.Val96Val	synonymous_variant	3/5	ENST00000265044.7	NP_009038.1	Q9UNL2-1
SSR3	NM_001308197.2 link	c.288T>C	p.Val96Val	synonymous_variant	3/5		NP_001295126.1	Q9UNL2-2
SSR3	NM_001308204.2 link	c.132T>C	p.Val44Val	synonymous_variant	3/5		NP_001295133.1	Q9UNL2C9J365
SSR3	NM_001308205.2 link	c.132T>C	p.Val44Val	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.288T>C	p.Val96Val	synonymous_variant	3/5	1	NM_007107.5	ENSP00000265044.2		Q9UNL2-1

Frequencies

GnomAD3 genomes

AF:

0.0137

AC:

2081

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0274

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00452

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000279

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0167

AC:

4189

AN:

250684

Hom.:

191

AF XY:

0.0165

AC XY:

2242

AN XY:

135562

show subpopulations

Gnomad AFR exome

AF:

0.0281

Gnomad AMR exome

AF:

0.00252

Gnomad ASJ exome

AF:

0.00248

Gnomad EAS exome

AF:

0.129

Gnomad SAS exome

AF:

0.0375

Gnomad FIN exome

AF:

0.0000939

Gnomad NFE exome

AF:

0.000308

Gnomad OTH exome

AF:

0.00965

GnomAD4 exome

AF:

0.00623

AC:

9104

AN:

1460996

Hom.:

342

Cov.:

AF XY:

0.00702

AC XY:

5101

AN XY:

726806

show subpopulations

Gnomad4 AFR exome

AF:

0.0294

Gnomad4 AMR exome

AF:

0.00277

Gnomad4 ASJ exome

AF:

0.00226

Gnomad4 EAS exome

AF:

0.0940

Gnomad4 SAS exome

AF:

0.0368

Gnomad4 FIN exome

AF:

0.0000757

Gnomad4 NFE exome

AF:

0.000193

Gnomad4 OTH exome

AF:

0.0132

GnomAD4 genome

AF:

0.0137

AC:

2089

AN:

152320

Hom.:

Cov.:

AF XY:

0.0141

AC XY:

1051

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0274

Gnomad4 AMR

AF:

0.00451

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.117

Gnomad4 SAS

AF:

0.0445

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000294

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.00473

Hom.:

Bravo

AF:

0.0149

Asia WGS

AF:

0.0600

AC:

209

AN:

3478

EpiCase

AF:

0.000382

EpiControl

AF:

0.000296

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	Jan 23, 2025	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.80

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

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