rs7210080

chr17-73170963-T-C

Variant summary

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

The NM_001050.3(SSTR2):c.*534T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 348,256 control chromosomes in the GnomAD database, including 16,931 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 0.33 (9236 hom., cov: 32)
  • Exomes 𝑓: 0.27 (7695 hom.)
• Consequence: SSTR2 NM_001050.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSTR2	NM_001050.3	c.*534T>C		3_prime_UTR_variant	2/2	ENST00000357585.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSTR2	ENST00000357585.4	c.*534T>C		3_prime_UTR_variant	2/2	1	NM_001050.3	P1

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49500 AN: 152004 Hom.: 9217 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.272 AC: 53348 AN: 196134 Hom.: 7695 Cov.: 0 AF XY: 0.279 AC XY: 29700 AN XY: 106594

Gnomad4 AFR exome AF: 0.524

Gnomad4 AMR exome AF: 0.383

Gnomad4 ASJ exome AF: 0.256

Gnomad4 EAS exome AF: 0.298

Gnomad4 SAS exome AF: 0.351

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.265

GnomAD4 genome AF: 0.326 AC: 49553 AN: 152122 Hom.: 9236 Cov.: 32 AF XY: 0.322 AC XY: 23935 AN XY: 74354

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.313

Alfa AF: 0.267 Hom.: 8536

Bravo AF: 0.350

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.59
Dann	Benign	0.57

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: rs7210080; hg19: chr17-71167102;