rs1868486

Positions:

• chr17-73165843-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.66).
• 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/exons	MANE	Protein	UniProt
SSTR2	NM_001050.3	c.-93+555G>T		intron_variant		ENST00000357585.4	NP_001041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSTR2	ENST00000357585.4	c.-93+555G>T		intron_variant		1	NM_001050.3	ENSP00000350198	P1
SSTR2	ENST00000579323.5	n.277+555G>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0868

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.315

Alfa AF: 0.336 Hom.: 1092

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

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: rs1868486; hg19: chr17-71161982;