rs34037914

chr16-1079501-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001172560.3(SSTR5):c.633C>T(p.Phe211=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 1,611,574 control chromosomes in the GnomAD database, including 3,364 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 0.048 (236 hom., cov: 33)
  • Exomes 𝑓: 0.062 (3128 hom.)
• Consequence: SSTR5 NM_001172560.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

SSTR5 (HGNC:11334): (somatostatin receptor 5) Somatostatin and its related peptide cortistatin exert multiple biological actions on normal and tumoral tissue targets by interacting with somatostatin receptors (SSTRs). The protein encoded by this gene is one of the SSTRs, which is a multi-pass membrane protein and belongs to the G-protein coupled receptor 1 family. The activity of this receptor is mediated by G proteins which inhibit adenylyl cyclase, and different regions of this receptor molecule are required for the activation of different signaling pathways. A mutation in this gene results in somatostatin analog resistance. Alternatively spliced transcript variants have been identified in this gene.[provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP7: Synonymous conserved (PhyloP=-2.4 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSTR5	NM_001172560.3	c.633C>T	p.Phe211=	synonymous_variant	2/2	ENST00000689027.1
SSTR5	NM_001053.4	c.633C>T	p.Phe211=	synonymous_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSTR5	ENST00000689027.1	c.633C>T	p.Phe211=	synonymous_variant	2/2		NM_001172560.3	P1
SSTR5	ENST00000293897.7	c.633C>T	p.Phe211=	synonymous_variant	1/1			P1
SSTR5	ENST00000711615.1	c.633C>T	p.Phe211=	synonymous_variant	2/2			P1
SSTR5	ENST00000711616.1	c.633C>T	p.Phe211=	synonymous_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.0476 AC: 7247 AN: 152200 Hom.: 234 Cov.: 33

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0468

GnomAD3 exomes AF: 0.0590 AC: 14592 AN: 247184 Hom.: 580 AF XY: 0.0575 AC XY: 7721 AN XY: 134300

Gnomad AFR exome AF: 0.0122

Gnomad AMR exome AF: 0.108

Gnomad ASJ exome AF: 0.0259

Gnomad EAS exome AF: 0.000384

Gnomad SAS exome AF: 0.0458

Gnomad FIN exome AF: 0.0737

Gnomad NFE exome AF: 0.0641

Gnomad OTH exome AF: 0.0577

GnomAD4 exome AF: 0.0624 AC: 91002 AN: 1459256 Hom.: 3128 Cov.: 32 AF XY: 0.0617 AC XY: 44786 AN XY: 725910

Gnomad4 AFR exome AF: 0.0113

Gnomad4 AMR exome AF: 0.103

Gnomad4 ASJ exome AF: 0.0263

Gnomad4 EAS exome AF: 0.000782

Gnomad4 SAS exome AF: 0.0476

Gnomad4 FIN exome AF: 0.0730

Gnomad4 NFE exome AF: 0.0666

Gnomad4 OTH exome AF: 0.0522

GnomAD4 genome AF: 0.0476 AC: 7257 AN: 152318 Hom.: 236 Cov.: 33 AF XY: 0.0481 AC XY: 3579 AN XY: 74472

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0670

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0404

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.0650

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0560 Hom.: 142

Bravo AF: 0.0460

Asia WGS AF: 0.0220 AC: 76 AN: 3478

EpiCase AF: 0.0580

EpiControl AF: 0.0554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.3
Dann	Benign	0.89

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: rs34037914; hg19: chr16-1129501; COSMIC: COSV53511256; COSMIC: COSV53511256;