rs1176761

Variant names:

• chr11-113942891-T-A
• rs1176761
• NM_006028.5:c.697-91T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-113942891-T-A
• chr11-113942891-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006028.5(HTR3B):​c.697-91T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 1,030,146 control chromosomes in the GnomAD database, including 2,048 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 0.086 (917 hom., cov: 32)
  • Exomes 𝑓: 0.039 (1131 hom.)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR3B	NM_006028.5	c.697-91T>A		intron_variant	Intron 6 of 8	ENST00000260191.8	NP_006019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR3B	ENST00000260191.8	c.697-91T>A		intron_variant	Intron 6 of 8	1	NM_006028.5	ENSP00000260191.2
HTR3B	ENST00000537778.5	c.664-91T>A		intron_variant	Intron 5 of 7	1		ENSP00000443118.1
HTR3B	ENST00000543092.1	c.481-1682T>A		intron_variant	Intron 4 of 4	3		ENSP00000440894.1

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13046 AN: 152022 Hom.: 910 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.0390 AC: 34211 AN: 878006 Hom.: 1131 AF XY: 0.0385 AC XY: 17395 AN XY: 451446

African (AFR) AF: 0.195 AC: 4310 AN: 22056

American (AMR) AF: 0.0723 AC: 2646 AN: 36616

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 358 AN: 21432

East Asian (EAS) AF: 0.000460 AC: 16 AN: 34808

South Asian (SAS) AF: 0.0460 AC: 3206 AN: 69658

European-Finnish (FIN) AF: 0.0941 AC: 4722 AN: 50184

Middle Eastern (MID) AF: 0.0482 AC: 215 AN: 4458

European-Non Finnish (NFE) AF: 0.0283 AC: 16955 AN: 598106

Other (OTH) AF: 0.0438 AC: 1783 AN: 40688

GnomAD4 genome AF: 0.0860 AC: 13080 AN: 152140 Hom.: 917 Cov.: 32 AF XY: 0.0893 AC XY: 6644 AN XY: 74368

African (AFR) AF: 0.195 AC: 8075 AN: 41470

American (AMR) AF: 0.0870 AC: 1329 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 63 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4812

European-Finnish (FIN) AF: 0.101 AC: 1073 AN: 10586

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0314 AC: 2136 AN: 68016

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0264 Hom.: 27

Bravo AF: 0.0873

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.39
PhyloP100		-0.75
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: rs1176761; hg19: chr11-113813613;