rs1466113

Positions:

• chr17-73169179-C-G
• chr17-73169179-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001050.3(SSTR2):​c.-92-49C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,054,650 control chromosomes in the GnomAD database, including 192,653 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 0.64 (31600 hom., cov: 33)
  • Exomes 𝑓: 0.60 (161053 hom.)
• Consequence: SSTR2 NM_001050.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSTR2	NM_001050.3	c.-92-49C>G		intron_variant		ENST00000357585.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSTR2	ENST00000357585.4	c.-92-49C>G		intron_variant		1	NM_001050.3	P1
SSTR2	ENST00000579323.5	n.447-49C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97218 AN: 151990 Hom.: 31557 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.648

GnomAD4 exome AF: 0.595 AC: 537448 AN: 902542 Hom.: 161053 Cov.: 12 AF XY: 0.599 AC XY: 269261 AN XY: 449618

Gnomad4 AFR exome AF: 0.758

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.651

Gnomad4 EAS exome AF: 0.573

Gnomad4 SAS exome AF: 0.704

Gnomad4 FIN exome AF: 0.551

Gnomad4 NFE exome AF: 0.580

Gnomad4 OTH exome AF: 0.612

GnomAD4 genome AF: 0.640 AC: 97306 AN: 152108 Hom.: 31600 Cov.: 33 AF XY: 0.639 AC XY: 47529 AN XY: 74366

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.644

Alfa AF: 0.513 Hom.: 1474

Bravo AF: 0.652

Asia WGS AF: 0.663 AC: 2305 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	1.3
DANN	Benign	0.28

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: rs1466113; hg19: chr17-71165318;