rs1868486

Variant names:

• chr17-73165843-G-T
• rs1868486
• NM_001050.3:c.-93+555G>T

Variant summary

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

The NM_001050.3(SSTR2):​c.-93+555G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 150,096 control chromosomes in the GnomAD database, including 7,037 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 0.30 (7037 hom., cov: 27)
• Consequence: SSTR2 NM_001050.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 2 publications found

Genes affected

SSTR2 (HGNC:11331): (somatostatin receptor 2) Somatostatin acts at many sites to inhibit the release of many hormones and other secretory proteins. The biologic effects of somatostatin are probably mediated by a family of G protein-coupled receptors that are expressed in a tissue-specific manner. SSTR2 is a member of the superfamily of receptors having seven transmembrane segments and is expressed in highest levels in cerebrum and kidney. [provided by RefSeq, Jul 2008]

ENSG00000264860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR2	NM_001050.3	c.-93+555G>T		intron_variant	Intron 1 of 1	ENST00000357585.4	NP_001041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR2	ENST00000357585.4	c.-93+555G>T		intron_variant	Intron 1 of 1	1	NM_001050.3	ENSP00000350198.2
SSTR2	ENST00000579323.5	n.277+555G>T		intron_variant	Intron 1 of 2	4
ENSG00000264860	ENST00000580671.1	n.312+555G>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.299 AC: 44883 AN: 149976 Hom.: 7031 Cov.: 27

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.299 AC: 44911 AN: 150096 Hom.: 7037 Cov.: 27 AF XY: 0.300 AC XY: 21927 AN XY: 73090

African (AFR) AF: 0.230 AC: 9402 AN: 40836

American (AMR) AF: 0.294 AC: 4399 AN: 14974

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1222 AN: 3456

East Asian (EAS) AF: 0.0868 AC: 438 AN: 5048

South Asian (SAS) AF: 0.342 AC: 1609 AN: 4708

European-Finnish (FIN) AF: 0.358 AC: 3657 AN: 10226

Middle Eastern (MID) AF: 0.229 AC: 66 AN: 288

European-Non Finnish (NFE) AF: 0.343 AC: 23212 AN: 67580

Other (OTH) AF: 0.315 AC: 654 AN: 2076

Alfa AF: 0.318 Hom.: 11537

Bravo AF: 0.288

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.1
DANN	Benign	0.88
PhyloP100		-0.45
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: rs1868486; hg19: chr17-71161982;