rs3773714

Variant names:

• chr3-156542177-A-T
• rs3773714
• NM_007107.5:c.*1026T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SSR3	NM_007107.5	c.*1026T>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000265044.7	NP_009038.1
SSR3	NM_001308197.2	c.*1026T>A		3_prime_UTR_variant	Exon 5 of 5		NP_001295126.1
SSR3	NM_001308204.2	c.*1026T>A		3_prime_UTR_variant	Exon 5 of 5		NP_001295133.1
SSR3	NM_001308205.2	c.*1026T>A		3_prime_UTR_variant	Exon 5 of 5		NP_001295134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSR3	ENST00000265044.7	c.*1026T>A		3_prime_UTR_variant	Exon 5 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0649 AC: 2695 AN: 41544

American (AMR) AF: 0.139 AC: 2121 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1101 AN: 5186

South Asian (SAS) AF: 0.195 AC: 938 AN: 4820

European-Finnish (FIN) AF: 0.0976 AC: 1035 AN: 10600

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8646 AN: 68000

Other (OTH) AF: 0.139 AC: 293 AN: 2112

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
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3773714; hg19: chr3-156259966;