Variant rs2276305 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006028.5(HTR3B):c.462G>A(p.Ala154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0301 in 1,613,556 control chromosomes in the GnomAD database, including 3,860 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 0.059 ( 639 hom., cov: 33)

Exomes 𝑓: 0.027 ( 3221 hom. )

Consequence

HTR3B
NM_006028.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

Variant links:

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]

HTR3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP7

Synonymous conserved (PhyloP=-2.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	NM_006028.5 linkuse as main transcript	c.462G>A	p.Ala154=	synonymous_variant	5/9	ENST00000260191.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR3B	ENST00000260191.8 linkuse as main transcript	c.462G>A	p.Ala154=	synonymous_variant	5/9	1	NM_006028.5	P2	O95264-1
HTR3B	ENST00000537778.5 linkuse as main transcript	c.429G>A	p.Ala143=	synonymous_variant	4/8	1		A2	O95264-2
HTR3B	ENST00000543092.1 linkuse as main transcript	c.249G>A	p.Ala83=	synonymous_variant	3/5	3

Frequencies

GnomAD3 genomes

AF:

0.0591

AC:

8982

AN:

152088

Hom.:

631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0996

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.0135

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.0682

Gnomad FIN

AF:

0.00631

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00895

Gnomad OTH

AF:

0.0589

GnomAD3 exomes

AF:

0.0773

AC:

19437

AN:

251290

Hom.:

2391

AF XY:

0.0663

AC XY:

9002

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.261

Gnomad ASJ exome

AF:

0.0136

Gnomad EAS exome

AF:

0.307

Gnomad SAS exome

AF:

0.0553

Gnomad FIN exome

AF:

0.00578

Gnomad NFE exome

AF:

0.00750

Gnomad OTH exome

AF:

0.0506

GnomAD4 exome

AF:

0.0271

AC:

39631

AN:

1461350

Hom.:

3221

Cov.:

AF XY:

0.0266

AC XY:

19373

AN XY:

727022

show subpopulations

Gnomad4 AFR exome

AF:

0.0966

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.0141

Gnomad4 EAS exome

AF:

0.232

Gnomad4 SAS exome

AF:

0.0538

Gnomad4 FIN exome

AF:

0.00524

Gnomad4 NFE exome

AF:

0.00749

Gnomad4 OTH exome

AF:

0.0431

GnomAD4 genome

AF:

0.0592

AC:

9016

AN:

152206

Hom.:

639

Cov.:

AF XY:

0.0614

AC XY:

4569

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0996

Gnomad4 AMR

AF:

0.143

Gnomad4 ASJ

AF:

0.0135

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.0680

Gnomad4 FIN

AF:

0.00631

Gnomad4 NFE

AF:

0.00897

Gnomad4 OTH

AF:

0.0645

Alfa

AF:

0.0232

Hom.:

384

Bravo

AF:

0.0756

EpiCase

AF:

0.00873

EpiControl

AF:

0.00788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

1.1

DANN

Benign

0.41

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over