rs11214763

Variant names:

• chr11-113904173-G-A
• rs11214763
• XM_024448767.2:c.-243+5090G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024448767.2(HTR3B):​c.-243+5090G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,818 control chromosomes in the GnomAD database, including 2,178 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 (2178 hom., cov: 32)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 8 publications found

Genes affected

HTR3B (HGNC:5298): (5-hydroxytryptamine receptor 3B) The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit B of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor causes fast, depolarizing responses in neurons after activation. It is not functional as a homomeric complex, but a pentaheteromeric complex with subunit A (HTR3A) displays the full functional features of this receptor. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25115 AN: 151702 Hom.: 2176 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.165 AC: 25122 AN: 151818 Hom.: 2178 Cov.: 32 AF XY: 0.165 AC XY: 12276 AN XY: 74198

African (AFR) AF: 0.157 AC: 6484 AN: 41394

American (AMR) AF: 0.132 AC: 2006 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3468

East Asian (EAS) AF: 0.102 AC: 526 AN: 5170

South Asian (SAS) AF: 0.177 AC: 855 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1705 AN: 10518

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12111 AN: 67920

Other (OTH) AF: 0.181 AC: 381 AN: 2104

Alfa AF: 0.174 Hom.: 3770

Bravo AF: 0.160

Asia WGS AF: 0.115 AC: 400 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs11214763; hg19: chr11-113774895; COSMIC: COSV107278877;