Variant 3-156548853-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007107.5(SSR3):c.359+52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.981 in 1,579,454 control chromosomes in the GnomAD database, including 760,363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.98 ( 73819 hom., cov: 30)

Exomes 𝑓: 0.98 ( 686544 hom. )

Consequence

SSR3
NM_007107.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.267

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 3-156548853-C-T is Benign according to our data. Variant chr3-156548853-C-T is described in ClinVar as [Benign]. Clinvar id is 1601159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
SSR3	NM_007107.5 link	c.359+52G>A	intron_variant	ENST00000265044.7	NP_009038.1	Q9UNL2-1
SSR3	NM_001308197.2 link	c.398+13G>A	intron_variant		NP_001295126.1	Q9UNL2-2
SSR3	NM_001308204.2 link	c.203+52G>A	intron_variant		NP_001295133.1	Q9UNL2C9J365
SSR3	NM_001308205.2 link	c.203+52G>A	intron_variant		NP_001295134.1	Q9UNL2C9J365

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSR3	ENST00000265044.7 link	c.359+52G>A		intron_variant		1	NM_007107.5	ENSP00000265044.2		Q9UNL2-1

Frequencies

GnomAD3 genomes

AF:

0.985

AC:

149803

AN:

152138

Hom.:

73760

Cov.:

show subpopulations

Gnomad AFR

AF:

0.996

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.987

Gnomad ASJ

AF:

0.990

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.994

Gnomad FIN

AF:

0.953

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.979

Gnomad OTH

AF:

0.989

GnomAD3 exomes

AF:

0.984

AC:

217393

AN:

220922

Hom.:

106977

AF XY:

0.984

AC XY:

118313

AN XY:

120290

show subpopulations

Gnomad AFR exome

AF:

0.996

Gnomad AMR exome

AF:

0.991

Gnomad ASJ exome

AF:

0.991

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.994

Gnomad FIN exome

AF:

0.962

Gnomad NFE exome

AF:

0.979

Gnomad OTH exome

AF:

0.982

GnomAD4 exome

AF:

0.981

AC:

1399785

AN:

1427198

Hom.:

686544

Cov.:

AF XY:

0.981

AC XY:

695315

AN XY:

708826

show subpopulations

Gnomad4 AFR exome

AF:

0.997

Gnomad4 AMR exome

AF:

0.990

Gnomad4 ASJ exome

AF:

0.992

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.993

Gnomad4 FIN exome

AF:

0.964

Gnomad4 NFE exome

AF:

0.979

Gnomad4 OTH exome

AF:

0.982

GnomAD4 genome

AF:

0.985

AC:

149921

AN:

152256

Hom.:

73819

Cov.:

AF XY:

0.983

AC XY:

73165

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.997

Gnomad4 AMR

AF:

0.987

Gnomad4 ASJ

AF:

0.990

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.994

Gnomad4 FIN

AF:

0.953

Gnomad4 NFE

AF:

0.979

Gnomad4 OTH

AF:

0.989

Alfa

AF:

0.983

Hom.:

13946

Bravo

AF:

0.987

Asia WGS

AF:

0.996

AC:

3463

AN:

3478

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 03, 2025	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.3

DANN

Benign

0.40

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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