rs3891484

Variant names:

• chr11-113901867-A-G
• rs3891484
• XM_024448767.2:c.-243+2784A>G

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+2784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,228 control chromosomes in the GnomAD database, including 1,769 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 0.15 (1769 hom., cov: 32)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 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: 0.149 AC: 22626 AN: 152110 Hom.: 1767 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.149 AC: 22635 AN: 152228 Hom.: 1769 Cov.: 32 AF XY: 0.153 AC XY: 11358 AN XY: 74436

African (AFR) AF: 0.124 AC: 5170 AN: 41554

American (AMR) AF: 0.178 AC: 2713 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.170 AC: 879 AN: 5172

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4822

European-Finnish (FIN) AF: 0.182 AC: 1935 AN: 10608

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9410 AN: 68004

Other (OTH) AF: 0.143 AC: 303 AN: 2114

Alfa AF: 0.147 Hom.: 1382

Bravo AF: 0.144

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.54
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs3891484; hg19: chr11-113772589;