NM_001050.3:c.*534T>C

Variant names:

• chr17-73170963-T-C
• rs7210080
• NM_001050.3:c.*534T>C

Variant summary

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

The NM_001050.3(SSTR2):​c.*534T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 348,256 control chromosomes in the GnomAD database, including 16,931 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 (9236 hom., cov: 32)
  • Exomes 𝑓: 0.27 (7695 hom.)
• Consequence: SSTR2 NM_001050.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 15 publications found

Genes affected

SSTR2 (HGNC:11331): (somatostatin receptor 2) Somatostatin acts at many sites to inhibit the release of many hormones and other secretory proteins. The biologic effects of somatostatin are probably mediated by a family of G protein-coupled receptors that are expressed in a tissue-specific manner. SSTR2 is a member of the superfamily of receptors having seven transmembrane segments and is expressed in highest levels in cerebrum and kidney. [provided by RefSeq, Jul 2008]

ENSG00000264860 (HGNC:):

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 = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001050.3. 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
	SSTR2	NM_001050.3	MANE Select	c.*534T>C		3_prime_UTR	Exon 2 of 2	NP_001041.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR2	ENST00000357585.4	TSL:1 MANE Select	c.*534T>C		3_prime_UTR	Exon 2 of 2	ENSP00000350198.2
	ENSG00000264860	ENST00000580671.1	TSL:4	n.312+5675T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49500 AN: 152004 Hom.: 9217 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.272 AC: 53348 AN: 196134 Hom.: 7695 Cov.: 0 AF XY: 0.279 AC XY: 29700 AN XY: 106594

African (AFR) AF: 0.524 AC: 2685 AN: 5122

American (AMR) AF: 0.383 AC: 3918 AN: 10234

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 1052 AN: 4112

East Asian (EAS) AF: 0.298 AC: 2431 AN: 8164

South Asian (SAS) AF: 0.351 AC: 12312 AN: 35124

European-Finnish (FIN) AF: 0.161 AC: 3572 AN: 22158

Middle Eastern (MID) AF: 0.302 AC: 184 AN: 610

European-Non Finnish (NFE) AF: 0.244 AC: 24836 AN: 101712

Other (OTH) AF: 0.265 AC: 2358 AN: 8898

GnomAD4 genome AF: 0.326 AC: 49553 AN: 152122 Hom.: 9236 Cov.: 32 AF XY: 0.322 AC XY: 23935 AN XY: 74354

African (AFR) AF: 0.508 AC: 21078 AN: 41482

American (AMR) AF: 0.365 AC: 5576 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1611 AN: 5166

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4820

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10590

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16084 AN: 68000

Other (OTH) AF: 0.313 AC: 662 AN: 2116

Alfa AF: 0.272 Hom.: 11922

Bravo AF: 0.350

Asia WGS AF: 0.331 AC: 1149 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	0.59
DANN	Benign	0.57
PhyloP100		-0.69
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: rs7210080; hg19: chr17-71167102;