rs5756564

Variant names:

• chr22-37216063-T-C
• rs5756564
• XM_017028924.2:c.-612A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

RPL39P41 (HGNC:35941):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SSTR3	XM_017028924.2	c.-612A>G		5_prime_UTR_variant	Exon 1 of 3		XP_016884413.1
SSTR3	XM_005261721.5	c.-37+4344A>G		intron_variant	Intron 1 of 1		XP_005261778.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL39P41	ENST00000436709.1	n.-172A>G		upstream_gene_variant		6

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

African (AFR) AF: 0.179 AC: 7447 AN: 41502

American (AMR) AF: 0.254 AC: 3884 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3472

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5182

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4822

European-Finnish (FIN) AF: 0.306 AC: 3233 AN: 10574

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27484 AN: 67966

Other (OTH) AF: 0.309 AC: 653 AN: 2110

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs5756564; hg19: chr22-37612103;