chr16-1078406-C-T

Position:

• chr16-1078406-C-T

Variant summary

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

The NM_001172560.3(SSTR5):​c.-27-436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 175,934 control chromosomes in the GnomAD database, including 12,220 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 0.35 (10359 hom., cov: 33)
  • Exomes 𝑓: 0.37 (1861 hom.)
• Consequence: SSTR5 NM_001172560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSTR5	NM_001172560.3	c.-27-436C>T		intron_variant		ENST00000689027.1	NP_001166031.1
SSTR5-AS1	NR_027242.1	n.274+52G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSTR5	ENST00000689027.1	c.-27-436C>T		intron_variant			NM_001172560.3	ENSP00000508487	P1
SSTR5-AS1	ENST00000569832.6	n.254+52G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52941 AN: 152006 Hom.: 10361 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.367 AC: 8732 AN: 23810 Hom.: 1861 Cov.: 0 AF XY: 0.369 AC XY: 4483 AN XY: 12140

Gnomad4 AFR exome AF: 0.183

Gnomad4 AMR exome AF: 0.396

Gnomad4 ASJ exome AF: 0.341

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.341

Gnomad4 FIN exome AF: 0.388

Gnomad4 NFE exome AF: 0.403

Gnomad4 OTH exome AF: 0.325

GnomAD4 genome AF: 0.348 AC: 52954 AN: 152124 Hom.: 10359 Cov.: 33 AF XY: 0.350 AC XY: 26069 AN XY: 74380

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.366

Alfa AF: 0.414 Hom.: 15379

Bravo AF: 0.337

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3751830; hg19: chr16-1128406;