16-1081695-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172560.3. 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
	SSTR5	NM_001172560.3	MANE Select	c.*1732A>G		downstream_gene	N/A	NP_001166031.1
	SSTR5	NM_001053.4		c.*1732A>G		downstream_gene	N/A	NP_001044.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	ENST00000689027.1	MANE Select	c.*1732A>G		downstream_gene	N/A	ENSP00000508487.1
	SSTR5	ENST00000293897.7	TSL:6	c.*1732A>G		downstream_gene	N/A	ENSP00000293897.4
	SSTR5	ENST00000711615.1		c.*1732A>G		downstream_gene	N/A	ENSP00000518810.1

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

African (AFR) AF: 0.700 AC: 29043 AN: 41472

American (AMR) AF: 0.638 AC: 9743 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1638 AN: 3466

East Asian (EAS) AF: 0.135 AC: 689 AN: 5110

South Asian (SAS) AF: 0.493 AC: 2372 AN: 4808

European-Finnish (FIN) AF: 0.653 AC: 6879 AN: 10542

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41954 AN: 67924

Other (OTH) AF: 0.600 AC: 1265 AN: 2108

Alfa AF: 0.594 Hom.: 20236

Bravo AF: 0.623

Asia WGS AF: 0.326 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.27
PhyloP100		0.94

Splicing

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

Other links and lift over

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