rs998571

Positions:

• chr17-73169153-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SSTR2	NM_001050.3	c.-92-75A>G		intron_variant		ENST00000357585.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSTR2	ENST00000357585.4	c.-92-75A>G		intron_variant		1	NM_001050.3	P1
SSTR2	ENST00000579323.5	n.447-75A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR exome AF: 0.233

Gnomad4 AMR exome AF: 0.264

Gnomad4 ASJ exome AF: 0.364

Gnomad4 EAS exome AF: 0.0731

Gnomad4 SAS exome AF: 0.326

Gnomad4 FIN exome AF: 0.351

Gnomad4 NFE exome AF: 0.339

Gnomad4 OTH exome AF: 0.315

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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0848

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.312

Alfa AF: 0.316 Hom.: 2778

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

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: rs998571; hg19: chr17-71165292; COSMIC: COSV59534967;