rs3782025

Positions:

• chr11-113936885-G-A
• chr11-113936885-G-C
• chr11-113936885-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006028.5(HTR3B):​c.696+3792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,894 control chromosomes in the GnomAD database, including 23,542 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 0.55 (23542 hom., cov: 31)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.50

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR3B	NM_006028.5	c.696+3792G>A		intron_variant		ENST00000260191.8	NP_006019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR3B	ENST00000260191.8	c.696+3792G>A		intron_variant		1	NM_006028.5	ENSP00000260191	P2
HTR3B	ENST00000537778.5	c.663+3792G>A		intron_variant		1		ENSP00000443118	A2
HTR3B	ENST00000543092.1	c.482+3792G>A		intron_variant		3		ENSP00000440894

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84126 AN: 151776 Hom.: 23515 Cov.: 31

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.554 AC: 84191 AN: 151894 Hom.: 23542 Cov.: 31 AF XY: 0.555 AC XY: 41198 AN XY: 74238

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.581

Alfa AF: 0.538 Hom.: 14124

Bravo AF: 0.560

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	20
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3782025; hg19: chr11-113807607; COSMIC: COSV52747960;