Variant 3-156544443-C-G 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.360-4G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,561,872 control chromosomes in the GnomAD database, including 54,289 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 6872 hom., cov: 32)

Exomes 𝑓: 0.26 ( 47417 hom. )

Consequence

SSR3
NM_007107.5 splice_region, intron

Scores

Splicing: ADA: 0.000007888

Clinical Significance

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

Conservation

PhyloP100: -0.394

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=-0.85).

BP6

Variant 3-156544443-C-G is Benign according to our data. Variant chr3-156544443-C-G is described in ClinVar as [Benign]. Clinvar id is 1600159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
SSR3	NM_007107.5 link	c.360-4G>C	splice_region_variant, intron_variant	ENST00000265044.7	NP_009038.1	Q9UNL2-1
SSR3	NM_001308197.2 link	c.399-4G>C	splice_region_variant, intron_variant		NP_001295126.1	Q9UNL2-2
SSR3	NM_001308204.2 link	c.204-4G>C	splice_region_variant, intron_variant		NP_001295133.1	Q9UNL2C9J365
SSR3	NM_001308205.2 link	c.204-4G>C	splice_region_variant, intron_variant		NP_001295134.1	Q9UNL2C9J365

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSR3	ENST00000265044.7 link	c.360-4G>C		splice_region_variant, intron_variant		1	NM_007107.5	ENSP00000265044.2		Q9UNL2-1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44760

AN:

151898

Hom.:

6840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.306

GnomAD3 exomes

AF:

0.280

AC:

62406

AN:

223254

Hom.:

8947

AF XY:

0.277

AC XY:

33529

AN XY:

120870

show subpopulations

Gnomad AFR exome

AF:

0.378

Gnomad AMR exome

AF:

0.271

Gnomad ASJ exome

AF:

0.240

Gnomad EAS exome

AF:

0.362

Gnomad SAS exome

AF:

0.314

Gnomad FIN exome

AF:

0.278

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.267

GnomAD4 exome

AF:

0.256

AC:

361506

AN:

1409856

Hom.:

47417

Cov.:

AF XY:

0.257

AC XY:

179650

AN XY:

698466

show subpopulations

Gnomad4 AFR exome

AF:

0.390

Gnomad4 AMR exome

AF:

0.275

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.317

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.275

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.295

AC:

44853

AN:

152016

Hom.:

6872

Cov.:

AF XY:

0.297

AC XY:

22096

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.377

Gnomad4 AMR

AF:

0.274

Gnomad4 ASJ

AF:

0.234

Gnomad4 EAS

AF:

0.367

Gnomad4 SAS

AF:

0.312

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.255

Hom.:

1679

Bravo

AF:

0.296

Asia WGS

AF:

0.382

AC:

1327

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

-0.85

CADD

Benign

0.35

DANN

Benign

0.50

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0000079

dbscSNV1_RF

Benign

0.0

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