rs3782025

Variant names:

• chr11-113936885-G-A
• rs3782025
• NM_006028.5:c.696+3792G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 34 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=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006028.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	NM_006028.5	MANE Select	c.696+3792G>A		intron	N/A	NP_006019.1
	HTR3B	NM_001363563.2		c.663+3792G>A		intron	N/A	NP_001350492.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	ENST00000260191.8	TSL:1 MANE Select	c.696+3792G>A		intron	N/A	ENSP00000260191.2
	HTR3B	ENST00000537778.5	TSL:1	c.663+3792G>A		intron	N/A	ENSP00000443118.1
	HTR3B	ENST00000543092.1	TSL:3	c.480+3792G>A		intron	N/A	ENSP00000440894.1

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

African (AFR) AF: 0.555 AC: 22971 AN: 41400

American (AMR) AF: 0.599 AC: 9144 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3466

East Asian (EAS) AF: 0.699 AC: 3605 AN: 5158

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4818

European-Finnish (FIN) AF: 0.486 AC: 5125 AN: 10544

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36197 AN: 67924

Other (OTH) AF: 0.581 AC: 1226 AN: 2110

Alfa AF: 0.537 Hom.: 22773

Bravo AF: 0.560

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	20
DANN	Benign	0.81
PhyloP100		3.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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