rs5756564

Positions:

• chr22-37216063-T-C
• chr22-37216063-T-G

Variant summary

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

The XM_017028924.2(SSTR3):​c.-612A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,114 control chromosomes in the GnomAD database, including 7,799 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 0.30 (7799 hom., cov: 32)
• Consequence: SSTR3 XM_017028924.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

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]

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSTR3	XM_017028924.2	c.-612A>G		5_prime_UTR_variant	1/3		XP_016884413.1
SSTR3	XM_005261721.5	c.-37+4344A>G		intron_variant			XP_005261778.1
		n.37216063T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45719 AN: 151994 Hom.: 7804 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.300 AC: 45705 AN: 152114 Hom.: 7799 Cov.: 32 AF XY: 0.291 AC XY: 21676 AN XY: 74364

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.309

Alfa AF: 0.199 Hom.: 421

Bravo AF: 0.290

Asia WGS AF: 0.153 AC: 530 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	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756564; hg19: chr22-37612103;