rs7220818

Positions:

• chr17-73170562-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.*133A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,144,846 control chromosomes in the GnomAD database, including 43,242 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 0.29 (7092 hom., cov: 31)
  • Exomes 𝑓: 0.26 (36150 hom.)
• Consequence: SSTR2 NM_001050.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSTR2	NM_001050.3	c.*133A>G		3_prime_UTR_variant	2/2	ENST00000357585.4	NP_001041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSTR2	ENST00000357585.4	c.*133A>G		3_prime_UTR_variant	2/2	1	NM_001050.3	ENSP00000350198.2
ENSG00000264860	ENST00000580671.1	n.312+5274A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44726 AN: 151702 Hom.: 7077 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.260 AC: 258171 AN: 993026 Hom.: 36150 Cov.: 13 AF XY: 0.262 AC XY: 133269 AN XY: 508198

Gnomad4 AFR exome AF: 0.390

Gnomad4 AMR exome AF: 0.444

Gnomad4 ASJ exome AF: 0.263

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.364

Gnomad4 FIN exome AF: 0.162

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.295 AC: 44776 AN: 151820 Hom.: 7092 Cov.: 31 AF XY: 0.293 AC XY: 21764 AN XY: 74208

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.304

Alfa AF: 0.281 Hom.: 1728

Bravo AF: 0.317

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.1
DANN	Benign	0.84

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: rs7220818; hg19: chr17-71166701;