rs3773714

Positions:

• chr3-156542177-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007107.5(SSR3):​c.*1026T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,234 control chromosomes in the GnomAD database, including 1,109 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.11 (1109 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SSR3 NM_007107.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSR3	NM_007107.5	c.*1026T>A		3_prime_UTR_variant	5/5	ENST00000265044.7	NP_009038.1
SSR3	NM_001308197.2	c.*1026T>A		3_prime_UTR_variant	5/5		NP_001295126.1
SSR3	NM_001308204.2	c.*1026T>A		3_prime_UTR_variant	5/5		NP_001295133.1
SSR3	NM_001308205.2	c.*1026T>A		3_prime_UTR_variant	5/5		NP_001295134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSR3	ENST00000265044	c.*1026T>A		3_prime_UTR_variant	5/5	1	NM_007107.5	ENSP00000265044.2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17313 AN: 152116 Hom.: 1100 Cov.: 33

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.133

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.114 AC: 17336 AN: 152234 Hom.: 1109 Cov.: 33 AF XY: 0.115 AC XY: 8543 AN XY: 74432

Gnomad4 AFR AF: 0.0649

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.139

Alfa AF: 0.111 Hom.: 136

Bravo AF: 0.111

Asia WGS AF: 0.227 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.79

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

Other links and lift over

dbSNP: rs3773714; hg19: chr3-156259966;