16-1076679-T-G

Position:

• chr16-1076679-T-G

Variant summary

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

The NM_001172560.3(SSTR5):​c.-27-2163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,068 control chromosomes in the GnomAD database, including 2,644 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 0.17 (2644 hom., cov: 31)
• Consequence: SSTR5 NM_001172560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSTR5	NM_001172560.3	c.-27-2163T>G		intron_variant		ENST00000689027.1	NP_001166031.1
SSTR5-AS1	NR_027242.1	n.363+945A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1	c.-27-2163T>G		intron_variant			NM_001172560.3	ENSP00000508487.1
SSTR5-AS1	ENST00000566499.1	n.339+945A>C		intron_variant		4
SSTR5-AS1	ENST00000569832.5	n.305+945A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25315 AN: 151950 Hom.: 2645 Cov.: 31

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.167 AC: 25329 AN: 152068 Hom.: 2644 Cov.: 31 AF XY: 0.170 AC XY: 12597 AN XY: 74282

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.146

Alfa AF: 0.189 Hom.: 3490

Bravo AF: 0.154

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs550713; hg19: chr16-1126679;