chr16-1079912-A-G

Variant names:

• chr16-1079912-A-G
• rs642249
• NM_001172560.3:c.1044A>G

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.1044A>G​(p.Pro348Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 1,606,566 control chromosomes in the GnomAD database, including 747,450 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 0.96 (69747 hom., cov: 36)
  • Exomes 𝑓: 0.96 (677703 hom.)
• Consequence: SSTR5 NM_001172560.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 17 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP7: Synonymous conserved (PhyloP=-0.177 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSTR5	NM_001172560.3	c.1044A>G	p.Pro348Pro	synonymous_variant	Exon 2 of 2	ENST00000689027.1	NP_001166031.1
SSTR5	NM_001053.4	c.1044A>G	p.Pro348Pro	synonymous_variant	Exon 1 of 1		NP_001044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1	c.1044A>G	p.Pro348Pro	synonymous_variant	Exon 2 of 2		NM_001172560.3	ENSP00000508487.1
SSTR5	ENST00000293897.7	c.1044A>G	p.Pro348Pro	synonymous_variant	Exon 1 of 1	6		ENSP00000293897.4
SSTR5	ENST00000711615.1	c.1044A>G	p.Pro348Pro	synonymous_variant	Exon 2 of 2			ENSP00000518810.1
SSTR5	ENST00000711616.1	c.*118A>G		3_prime_UTR_variant	Exon 2 of 2			ENSP00000518811.1

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145614 AN: 152216 Hom.: 69705 Cov.: 36

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.968

GnomAD2 exomes AF: 0.956 AC: 226852 AN: 237238 AF XY: 0.953

Gnomad AFR exome AF: 0.932

Gnomad AMR exome AF: 0.987

Gnomad ASJ exome AF: 0.977

Gnomad EAS exome AF: 0.931

Gnomad FIN exome AF: 0.972

Gnomad NFE exome AF: 0.970

Gnomad OTH exome AF: 0.967

GnomAD4 exome AF: 0.965 AC: 1403240 AN: 1454232 Hom.: 677703 Cov.: 76 AF XY: 0.962 AC XY: 695749 AN XY: 723110

African (AFR) AF: 0.932 AC: 31091 AN: 33370

American (AMR) AF: 0.986 AC: 43583 AN: 44184

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 25380 AN: 25942

East Asian (EAS) AF: 0.954 AC: 37712 AN: 39542

South Asian (SAS) AF: 0.882 AC: 75690 AN: 85798

European-Finnish (FIN) AF: 0.973 AC: 48847 AN: 50220

Middle Eastern (MID) AF: 0.985 AC: 5666 AN: 5750

European-Non Finnish (NFE) AF: 0.971 AC: 1077556 AN: 1109362

Other (OTH) AF: 0.961 AC: 57715 AN: 60064

GnomAD4 genome AF: 0.957 AC: 145709 AN: 152334 Hom.: 69747 Cov.: 36 AF XY: 0.956 AC XY: 71183 AN XY: 74480

African (AFR) AF: 0.938 AC: 38989 AN: 41578

American (AMR) AF: 0.981 AC: 15017 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3406 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4813 AN: 5162

South Asian (SAS) AF: 0.880 AC: 4248 AN: 4828

European-Finnish (FIN) AF: 0.969 AC: 10297 AN: 10630

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65743 AN: 68028

Other (OTH) AF: 0.961 AC: 2033 AN: 2116

Alfa AF: 0.964 Hom.: 35979

Bravo AF: 0.960

Asia WGS AF: 0.890 AC: 3094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs642249; hg19: chr16-1129912; COSMIC: COSV53511767; COSMIC: COSV53511767;