16-1063847-T-G

Variant names:

• chr16-1063847-T-G
• rs213656
• ENST00000711615.1:c.-1663T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000711615.1(SSTR5):​c.-1663T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,062 control chromosomes in the GnomAD database, including 18,523 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 0.47 (18523 hom., cov: 33)
• Consequence: SSTR5 ENST00000711615.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.48
• Publications: 10 publications found

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]

SSTR5-AS1 (HGNC:26502): (SSTR5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711615.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5-AS1	NR_027242.1		n.*234A>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	ENST00000711615.1		c.-1663T>G		upstream_gene	N/A	ENSP00000518810.1
	SSTR5-AS1	ENST00000565992.2	TSL:4	n.*240A>C		downstream_gene	N/A
	SSTR5-AS1	ENST00000569832.6	TSL:2	n.*234A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70993 AN: 151942 Hom.: 18530 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.467 AC: 70985 AN: 152062 Hom.: 18523 Cov.: 33 AF XY: 0.470 AC XY: 34921 AN XY: 74332

African (AFR) AF: 0.233 AC: 9668 AN: 41494

American (AMR) AF: 0.538 AC: 8223 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1606 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1838 AN: 4822

European-Finnish (FIN) AF: 0.666 AC: 7039 AN: 10572

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39461 AN: 67954

Other (OTH) AF: 0.482 AC: 1016 AN: 2110

Alfa AF: 0.537 Hom.: 25752

Bravo AF: 0.452

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.33
PhyloP100		-4.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs213656; hg19: chr16-1113847;