rs229566

Positions:

• chr22-37206091-G-A

Variant summary

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

The NM_001051.5(SSTR3):​c.*456C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 156,590 control chromosomes in the GnomAD database, including 12,314 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 0.39 (12051 hom., cov: 32)
  • Exomes 𝑓: 0.31 (263 hom.)
• Consequence: SSTR3 NM_001051.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

Genes affected

SSTR3 (HGNC:11332): (somatostatin receptor 3) This gene encodes a member of the somatostatin receptor protein family. Somatostatins are peptide hormones that regulate diverse cellular functions such as neurotransmission, cell proliferation, and endocrine signaling as well as inhibiting the release of many hormones and other secretory proteins. Somatostatin has two active forms of 14 and 28 amino acids. The biological effects of somatostatins are mediated by a family of G-protein coupled somatostatin receptors that are expressed in a tissue-specific manner. Somatostatin receptors form homodimers and heterodimers with other members of the superfamily as well as with other G-protein coupled receptors and receptor tyrosine kinases. This protein is functionally coupled to adenylyl cyclase. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

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 = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSTR3	NM_001051.5	c.*456C>T		3_prime_UTR_variant	2/2	ENST00000610913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSTR3	ENST00000610913.2	c.*456C>T		3_prime_UTR_variant	2/2	1	NM_001051.5	P1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59030 AN: 151912 Hom.: 12030 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.305 AC: 1392 AN: 4560 Hom.: 263 Cov.: 0 AF XY: 0.304 AC XY: 726 AN XY: 2388

Gnomad4 AFR exome AF: 0.396

Gnomad4 AMR exome AF: 0.267

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.313

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.312

Gnomad4 OTH exome AF: 0.340

GnomAD4 genome AF: 0.389 AC: 59100 AN: 152030 Hom.: 12051 Cov.: 32 AF XY: 0.382 AC XY: 28387 AN XY: 74312

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.362

Alfa AF: 0.372 Hom.: 2441

Bravo AF: 0.397

Asia WGS AF: 0.346 AC: 1201 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	0.48
DANN	Benign	0.41

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: rs229566; hg19: chr22-37602131;