rs998571

Variant names:

• chr17-73169153-A-G
• rs998571
• NM_001050.3:c.-92-75A>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.-92-75A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 759,488 control chromosomes in the GnomAD database, including 39,455 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 (7050 hom., cov: 33)
  • Exomes 𝑓: 0.32 (32405 hom.)
• Consequence: SSTR2 NM_001050.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 12 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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR2	NM_001050.3	c.-92-75A>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.-92-75A>G		intron_variant	Intron 1 of 1	1	NM_001050.3	ENSP00000350198.2
SSTR2	ENST00000579323.5	n.447-75A>G		intron_variant	Intron 2 of 2	4
ENSG00000264860	ENST00000580671.1	n.312+3865A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45145 AN: 152094 Hom.: 7044 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0850

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.319 AC: 193757 AN: 607276 Hom.: 32405 AF XY: 0.320 AC XY: 99615 AN XY: 311386

African (AFR) AF: 0.233 AC: 3553 AN: 15222

American (AMR) AF: 0.264 AC: 4958 AN: 18746

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 5352 AN: 14702

East Asian (EAS) AF: 0.0731 AC: 2324 AN: 31782

South Asian (SAS) AF: 0.326 AC: 15318 AN: 46936

European-Finnish (FIN) AF: 0.351 AC: 10493 AN: 29908

Middle Eastern (MID) AF: 0.301 AC: 694 AN: 2302

European-Non Finnish (NFE) AF: 0.339 AC: 141213 AN: 416366

Other (OTH) AF: 0.315 AC: 9852 AN: 31312

GnomAD4 genome AF: 0.297 AC: 45169 AN: 152212 Hom.: 7050 Cov.: 33 AF XY: 0.297 AC XY: 22108 AN XY: 74418

African (AFR) AF: 0.234 AC: 9734 AN: 41532

American (AMR) AF: 0.268 AC: 4104 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3472

East Asian (EAS) AF: 0.0848 AC: 440 AN: 5188

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4824

European-Finnish (FIN) AF: 0.357 AC: 3783 AN: 10586

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

European-Non Finnish (NFE) AF: 0.342 AC: 23241 AN: 67992

Other (OTH) AF: 0.312 AC: 659 AN: 2114

Alfa AF: 0.301 Hom.: 3805

Bravo AF: 0.286

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.9
DANN	Benign	0.79
PhyloP100		-0.39
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: rs998571; hg19: chr17-71165292; COSMIC: COSV59534967;