rs4820272

Variant names:

• chr22-37219574-G-A
• rs4820272
• XM_005261721.5:c.-37+833C>T

Variant summary

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

The XM_005261721.5(SSTR3):​c.-37+833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,068 control chromosomes in the GnomAD database, including 3,323 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 0.19 (3323 hom., cov: 32)
• Consequence: SSTR3 XM_005261721.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.98
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR3	XM_005261721.5	c.-37+833C>T		intron_variant	Intron 1 of 1		XP_005261778.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29259 AN: 151950 Hom.: 3312 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.193 AC: 29306 AN: 152068 Hom.: 3323 Cov.: 32 AF XY: 0.191 AC XY: 14187 AN XY: 74318

African (AFR) AF: 0.309 AC: 12803 AN: 41422

American (AMR) AF: 0.119 AC: 1822 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1506 AN: 5166

South Asian (SAS) AF: 0.122 AC: 589 AN: 4830

European-Finnish (FIN) AF: 0.149 AC: 1574 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9691 AN: 68000

Other (OTH) AF: 0.194 AC: 410 AN: 2114

Alfa AF: 0.164 Hom.: 466

Bravo AF: 0.197

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.059
DANN	Benign	0.68
PhyloP100		-5.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4820272; hg19: chr22-37615614;