rs4988479

Variant names:

• chr16-1078895-G-A
• rs4988479
• NM_001172560.3:c.27G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001172560.3(SSTR5):​c.27G>A​(p.Thr9Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00948 in 1,606,246 control chromosomes in the GnomAD database, including 252 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 0.0073 (21 hom., cov: 33)
  • Exomes 𝑓: 0.0097 (231 hom.)
• Consequence: SSTR5 NM_001172560.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP7: Synonymous conserved (PhyloP=-1.75 with no splicing effect.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR5	NM_001172560.3	c.27G>A	p.Thr9Thr	synonymous_variant	Exon 2 of 2	ENST00000689027.1	NP_001166031.1
SSTR5	NM_001053.4	c.27G>A	p.Thr9Thr	synonymous_variant	Exon 1 of 1		NP_001044.1
SSTR5-AS1	NR_027242.1	n.-164C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1	c.27G>A	p.Thr9Thr	synonymous_variant	Exon 2 of 2		NM_001172560.3	ENSP00000508487.1

Frequencies

GnomAD3 genomes AF: 0.00730 AC: 1111 AN: 152144 Hom.: 22 Cov.: 33

Gnomad AFR AF: 0.00101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00948

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.00886

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00772

Gnomad OTH AF: 0.00957

GnomAD2 exomes AF: 0.0128 AC: 3003 AN: 233704 AF XY: 0.0154

Gnomad AFR exome AF: 0.000921

Gnomad AMR exome AF: 0.00625

Gnomad ASJ exome AF: 0.00290

Gnomad EAS exome AF: 0.000559

Gnomad FIN exome AF: 0.00958

Gnomad NFE exome AF: 0.00655

Gnomad OTH exome AF: 0.0102

GnomAD4 exome AF: 0.00971 AC: 14114 AN: 1453986 Hom.: 231 Cov.: 29 AF XY: 0.0111 AC XY: 8060 AN XY: 723486

Gnomad4 AFR exome AF: 0.00129 AC: 43 AN: 33390

Gnomad4 AMR exome AF: 0.00677 AC: 302 AN: 44580

Gnomad4 ASJ exome AF: 0.00315 AC: 82 AN: 26062

Gnomad4 EAS exome AF: 0.000252 AC: 10 AN: 39618

Gnomad4 SAS exome AF: 0.0578 AC: 4973 AN: 85974

Gnomad4 FIN exome AF: 0.0115 AC: 552 AN: 47890

Gnomad4 NFE exome AF: 0.00682 AC: 7582 AN: 1111074

Gnomad4 Remaining exome AF: 0.00904 AC: 543 AN: 60076

GnomAD4 genome AF: 0.00727 AC: 1107 AN: 152260 Hom.: 21 Cov.: 33 AF XY: 0.00826 AC XY: 615 AN XY: 74454

Gnomad4 AFR AF: 0.00101 AC: 0.00101034 AN: 0.00101034

Gnomad4 AMR AF: 0.00947 AC: 0.0094697 AN: 0.0094697

Gnomad4 ASJ AF: 0.00260 AC: 0.00259516 AN: 0.00259516

Gnomad4 EAS AF: 0.00155 AC: 0.00155219 AN: 0.00155219

Gnomad4 SAS AF: 0.0541 AC: 0.0540821 AN: 0.0540821

Gnomad4 FIN AF: 0.00886 AC: 0.0088579 AN: 0.0088579

Gnomad4 NFE AF: 0.00772 AC: 0.00772059 AN: 0.00772059

Gnomad4 OTH AF: 0.00947 AC: 0.0094697 AN: 0.0094697

Alfa AF: 0.00641 Hom.: 4

Bravo AF: 0.00531

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.68
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

Publications

LitVar

Other links and lift over

dbSNP: rs4988479; hg19: chr16-1128895;