NM_001172560.3:c.*1732A>G

Variant names:

• chr16-1081695-A-G
• rs197056
• NM_001172560.3:c.*1732A>G

Variant summary

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

The NM_001172560.3(SSTR5):​c.*1732A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,914 control chromosomes in the GnomAD database, including 30,144 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 0.62 (30144 hom., cov: 32)
• Consequence: SSTR5 NM_001172560.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943

Genes affected

SSTR5 (HGNC:11334): (somatostatin receptor 5) Somatostatin and its related peptide cortistatin exert multiple biological actions on normal and tumoral tissue targets by interacting with somatostatin receptors (SSTRs). The protein encoded by this gene is one of the SSTRs, which is a multi-pass membrane protein and belongs to the G-protein coupled receptor 1 family. The activity of this receptor is mediated by G proteins which inhibit adenylyl cyclase, and different regions of this receptor molecule are required for the activation of different signaling pathways. A mutation in this gene results in somatostatin analog resistance. Alternatively spliced transcript variants have been identified in this gene.[provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR5	NM_001172560.3	c.*1732A>G		downstream_gene_variant		ENST00000689027.1	NP_001166031.1
SSTR5	NM_001053.4	c.*1732A>G		downstream_gene_variant			NP_001044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1	c.*1732A>G		downstream_gene_variant			NM_001172560.3	ENSP00000508487.1
SSTR5	ENST00000293897.6	c.*1732A>G		downstream_gene_variant		6		ENSP00000293897.4

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94113 AN: 151796 Hom.: 30113 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.620 AC: 94192 AN: 151914 Hom.: 30144 Cov.: 32 AF XY: 0.618 AC XY: 45862 AN XY: 74252

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.600

Alfa AF: 0.598 Hom.: 14182

Bravo AF: 0.623

Asia WGS AF: 0.326 AC: 1138 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	4.7
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs197056; hg19: chr16-1131695; COSMIC: COSV53513622;