XM_024448767.2:c.-243+550G>A

Variant names:

• chr11-113899633-G-A
• rs1176758
• XM_024448767.2:c.-243+550G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_024448767.2(HTR3B):​c.-243+550G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,144 control chromosomes in the GnomAD database, including 39,827 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 0.71 (39827 hom., cov: 33)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 5 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107967 AN: 152026 Hom.: 39764 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.710 AC: 108089 AN: 152144 Hom.: 39827 Cov.: 33 AF XY: 0.713 AC XY: 53006 AN XY: 74348

African (AFR) AF: 0.913 AC: 37940 AN: 41558

American (AMR) AF: 0.730 AC: 11166 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3466

East Asian (EAS) AF: 0.730 AC: 3786 AN: 5184

South Asian (SAS) AF: 0.710 AC: 3423 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6547 AN: 10544

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40683 AN: 67974

Other (OTH) AF: 0.722 AC: 1519 AN: 2104

Alfa AF: 0.630 Hom.: 41840

Bravo AF: 0.724

Asia WGS AF: 0.745 AC: 2591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Benign	0.67
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs1176758; hg19: chr11-113770355;