rs13053175

Variant names:

• chr22-37217269-C-T
• rs13053175
• XM_005261721.5:c.-37+3138G>A

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+3138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,118 control chromosomes in the GnomAD database, including 8,910 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 (8910 hom., cov: 33)
• Consequence: SSTR3 XM_005261721.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 15 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR3	XM_005261721.5	c.-37+3138G>A		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: 0.328 AC: 49813 AN: 151998 Hom.: 8914 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.327 AC: 49791 AN: 152118 Hom.: 8910 Cov.: 33 AF XY: 0.316 AC XY: 23507 AN XY: 74360

African (AFR) AF: 0.238 AC: 9853 AN: 41476

American (AMR) AF: 0.279 AC: 4266 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3468

East Asian (EAS) AF: 0.0891 AC: 462 AN: 5188

South Asian (SAS) AF: 0.246 AC: 1187 AN: 4822

European-Finnish (FIN) AF: 0.298 AC: 3152 AN: 10564

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28629 AN: 67986

Other (OTH) AF: 0.336 AC: 710 AN: 2114

Alfa AF: 0.383 Hom.: 38349

Bravo AF: 0.321

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.74
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs13053175; hg19: chr22-37613309;