NM_001050.3:c.-92-1698A>G

Variant names:

• chr17-73167530-A-G
• rs714925
• NM_001050.3:c.-92-1698A>G

Variant summary

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

The NM_001050.3(SSTR2):​c.-92-1698A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,048 control chromosomes in the GnomAD database, including 7,173 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 (7173 hom., cov: 32)
• Consequence: SSTR2 NM_001050.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR2	NM_001050.3	c.-92-1698A>G		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.-92-1698A>G		intron_variant	Intron 1 of 1	1	NM_001050.3	ENSP00000350198.2
SSTR2	ENST00000579323.5	n.278-436A>G		intron_variant	Intron 1 of 2	4
ENSG00000264860	ENST00000580671.1	n.312+2242A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45541 AN: 151930 Hom.: 7167 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.300 AC: 45564 AN: 152048 Hom.: 7173 Cov.: 32 AF XY: 0.301 AC XY: 22355 AN XY: 74310

African (AFR) AF: 0.228 AC: 9458 AN: 41490

American (AMR) AF: 0.295 AC: 4500 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3466

East Asian (EAS) AF: 0.0833 AC: 431 AN: 5176

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4812

European-Finnish (FIN) AF: 0.362 AC: 3821 AN: 10554

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23467 AN: 67966

Other (OTH) AF: 0.315 AC: 665 AN: 2114

Alfa AF: 0.329 Hom.: 2089

Bravo AF: 0.288

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs714925; hg19: chr17-71163669;