chr11-113903224-C-T

Variant names:

• chr11-113903224-C-T
• rs10789970
• XM_024448767.2:c.-243+4141C>T

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+4141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,684 control chromosomes in the GnomAD database, including 20,274 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 0.51 (20274 hom., cov: 30)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 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: 0.508 AC: 76956 AN: 151566 Hom.: 20230 Cov.: 30

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.508 AC: 77058 AN: 151684 Hom.: 20274 Cov.: 30 AF XY: 0.511 AC XY: 37907 AN XY: 74120

African (AFR) AF: 0.634 AC: 26225 AN: 41332

American (AMR) AF: 0.576 AC: 8785 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3195 AN: 5132

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4818

European-Finnish (FIN) AF: 0.459 AC: 4816 AN: 10486

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28438 AN: 67888

Other (OTH) AF: 0.510 AC: 1070 AN: 2098

Alfa AF: 0.449 Hom.: 60686

Bravo AF: 0.521

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.22
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs10789970; hg19: chr11-113773946;