rs3891484

Positions:

• chr11-113901867-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR3B	XM_024448767.2	c.-243+2784A>G		intron_variant			XP_024304535.1
		n.113901867A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.143

Alfa AF: 0.149 Hom.: 1067

Bravo AF: 0.144

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3891484; hg19: chr11-113772589;