rs535338

Variant names:

• chr16-1077199-A-G
• rs535338
• NM_001172560.3:c.-27-1643A>G

Variant summary

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

The ENST00000689027.1(SSTR5):​c.-27-1643A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,132 control chromosomes in the GnomAD database, including 2,545 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 0.16 (2545 hom., cov: 32)
• Consequence: SSTR5 ENST00000689027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 4 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]

SSTR5-AS1 (HGNC:26502): (SSTR5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689027.1. 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.-27-1643A>G		intron	N/A	NP_001166031.1
	SSTR5-AS1	NR_027242.1		n.363+425T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	ENST00000689027.1	MANE Select	c.-27-1643A>G		intron	N/A	ENSP00000508487.1
	SSTR5	ENST00000711615.1		c.-27-1643A>G		intron	N/A	ENSP00000518810.1
	SSTR5-AS1	ENST00000566499.1	TSL:4	n.339+425T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24819 AN: 152014 Hom.: 2545 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.163 AC: 24839 AN: 152132 Hom.: 2545 Cov.: 32 AF XY: 0.167 AC XY: 12402 AN XY: 74368

African (AFR) AF: 0.0738 AC: 3065 AN: 41518

American (AMR) AF: 0.153 AC: 2341 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.101 AC: 524 AN: 5174

South Asian (SAS) AF: 0.0886 AC: 427 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3526 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14000 AN: 67972

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.170 Hom.: 667

Bravo AF: 0.150

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.53
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs535338; hg19: chr16-1127199;