rs1466113

Variant names:

• chr17-73169179-C-G
• rs1466113
• NM_001050.3:c.-92-49C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_001050.3(SSTR2):​c.-92-49C>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
• Publications: 19 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 (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR2	NM_001050.3	c.-92-49C>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.-92-49C>G		intron_variant	Intron 1 of 1	1	NM_001050.3	ENSP00000350198.2
SSTR2	ENST00000579323.5	n.447-49C>G		intron_variant	Intron 2 of 2	4
ENSG00000264860	ENST00000580671.1	n.312+3891C>G		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.758 AC: 15675 AN: 20682

American (AMR) AF: 0.685 AC: 13236 AN: 19328

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 10818 AN: 16610

East Asian (EAS) AF: 0.573 AC: 18924 AN: 33046

South Asian (SAS) AF: 0.704 AC: 37958 AN: 53888

European-Finnish (FIN) AF: 0.551 AC: 17046 AN: 30922

Middle Eastern (MID) AF: 0.635 AC: 1818 AN: 2862

European-Non Finnish (NFE) AF: 0.580 AC: 396942 AN: 684312

Other (OTH) AF: 0.612 AC: 25031 AN: 40892

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

African (AFR) AF: 0.749 AC: 31069 AN: 41504

American (AMR) AF: 0.660 AC: 10095 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2227 AN: 3472

East Asian (EAS) AF: 0.527 AC: 2722 AN: 5166

South Asian (SAS) AF: 0.714 AC: 3442 AN: 4824

European-Finnish (FIN) AF: 0.549 AC: 5804 AN: 10570

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39802 AN: 67964

Other (OTH) AF: 0.644 AC: 1360 AN: 2112

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
PhyloP100		-0.41
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: rs1466113; hg19: chr17-71165318;