chr22-37206091-G-A

Variant names:

• chr22-37206091-G-A
• rs229566
• NM_001051.5:c.*456C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001051.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR3	NM_001051.5	MANE Select	c.*456C>T		3_prime_UTR	Exon 2 of 2	NP_001042.1
	SSTR3	NM_001278687.2		c.*456C>T		3_prime_UTR	Exon 2 of 2	NP_001265616.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR3	ENST00000610913.2	TSL:1 MANE Select	c.*456C>T		3_prime_UTR	Exon 2 of 2	ENSP00000480971.1

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

African (AFR) AF: 0.396 AC: 42 AN: 106

American (AMR) AF: 0.267 AC: 80 AN: 300

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 24 AN: 122

East Asian (EAS) AF: 0.250 AC: 20 AN: 80

South Asian (SAS) AF: 0.313 AC: 52 AN: 166

European-Finnish (FIN) AF: 0.235 AC: 38 AN: 162

Middle Eastern (MID) AF: 0.250 AC: 3 AN: 12

European-Non Finnish (NFE) AF: 0.312 AC: 1044 AN: 3350

Other (OTH) AF: 0.340 AC: 89 AN: 262

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

African (AFR) AF: 0.533 AC: 22092 AN: 41422

American (AMR) AF: 0.361 AC: 5516 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1261 AN: 5162

South Asian (SAS) AF: 0.379 AC: 1830 AN: 4824

European-Finnish (FIN) AF: 0.284 AC: 3006 AN: 10590

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23346 AN: 67948

Other (OTH) AF: 0.362 AC: 767 AN: 2116

Alfa AF: 0.376 Hom.: 2560

Bravo AF: 0.397

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.41
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs229566; hg19: chr22-37602131;