16-1076679-T-G

Variant names:

• chr16-1076679-T-G
• rs550713
• NM_001172560.3:c.-27-2163T>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.-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
• Publications: 13 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	NM_001172560.3	MANE Select	c.-27-2163T>G		intron	N/A	NP_001166031.1	P35346
	SSTR5-AS1	NR_027242.1		n.363+945A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSTR5	ENST00000689027.1	MANE Select	c.-27-2163T>G		intron	N/A	ENSP00000508487.1	P35346
	SSTR5	ENST00000711615.1		c.-27-2163T>G		intron	N/A	ENSP00000518810.1	P35346
	SSTR5	ENST00000886519.1		c.-27-2163T>G		intron	N/A	ENSP00000556578.1

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

African (AFR) AF: 0.0699 AC: 2903 AN: 41550

American (AMR) AF: 0.159 AC: 2424 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3468

East Asian (EAS) AF: 0.101 AC: 519 AN: 5122

South Asian (SAS) AF: 0.0899 AC: 433 AN: 4816

European-Finnish (FIN) AF: 0.335 AC: 3523 AN: 10532

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14478 AN: 67980

Other (OTH) AF: 0.146 AC: 308 AN: 2110

Alfa AF: 0.187 Hom.: 4442

Bravo AF: 0.154

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.7
DANN	Benign	0.81
PhyloP100		0.45
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: rs550713; hg19: chr16-1126679;