Variant rs17116138 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006028.5(HTR3B):c.547G>A(p.Val183Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 1,613,786 control chromosomes in the GnomAD database, including 1,311 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.053 ( 276 hom., cov: 32)

Exomes 𝑓: 0.033 ( 1035 hom. )

Consequence

HTR3B
NM_006028.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.644

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001542449).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0792 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.547G>A	p.Val183Ile	missense_variant	6/9	ENST00000260191.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR3B	ENST00000260191.8 linkuse as main transcript	c.547G>A	p.Val183Ile	missense_variant	6/9	1	NM_006028.5	P2	O95264-1
HTR3B	ENST00000537778.5 linkuse as main transcript	c.514G>A	p.Val172Ile	missense_variant	5/8	1		A2	O95264-2
HTR3B	ENST00000543092.1 linkuse as main transcript	c.334G>A	p.Val112Ile	missense_variant	4/5	3

Frequencies

GnomAD3 genomes

AF:

0.0530

AC:

8055

AN:

152082

Hom.:

275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0815

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0711

Gnomad ASJ

AF:

0.0182

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0460

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0310

Gnomad OTH

AF:

0.0469

GnomAD3 exomes

AF:

0.0438

AC:

10992

AN:

251098

Hom.:

350

AF XY:

0.0416

AC XY:

5651

AN XY:

135698

show subpopulations

Gnomad AFR exome

AF:

0.0830

Gnomad AMR exome

AF:

0.0672

Gnomad ASJ exome

AF:

0.0152

Gnomad EAS exome

AF:

0.000979

Gnomad SAS exome

AF:

0.0449

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.0296

Gnomad OTH exome

AF:

0.0389

GnomAD4 exome

AF:

0.0335

AC:

48892

AN:

1461586

Hom.:

1035

Cov.:

AF XY:

0.0336

AC XY:

24466

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.0806

Gnomad4 AMR exome

AF:

0.0656

Gnomad4 ASJ exome

AF:

0.0167

Gnomad4 EAS exome

AF:

0.000504

Gnomad4 SAS exome

AF:

0.0462

Gnomad4 FIN exome

AF:

0.0937

Gnomad4 NFE exome

AF:

0.0284

Gnomad4 OTH exome

AF:

0.0331

GnomAD4 genome

AF:

0.0530

AC:

8063

AN:

152200

Hom.:

276

Cov.:

AF XY:

0.0565

AC XY:

4200

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0815

Gnomad4 AMR

AF:

0.0712

Gnomad4 ASJ

AF:

0.0182

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0458

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.0310

Gnomad4 OTH

AF:

0.0464

Alfa

AF:

0.0323

Hom.:

185

Bravo

AF:

0.0494

TwinsUK

AF:

0.0267

AC:

ALSPAC

AF:

0.0291

AC:

112

ESP6500AA

AF:

0.0795

AC:

350

ESP6500EA

AF:

0.0317

AC:

272

ExAC

AF:

0.0418

AC:

5069

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.0274

EpiControl

AF:

0.0228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.48

Cadd

Benign

9.4

Dann

Benign

0.71

DEOGEN2

Benign

0.021

T;.

Eigen

Benign

-0.93

Eigen_PC

Benign

-0.77

FATHMM_MKL

Benign

0.093

LIST_S2

Benign

0.55

T;T

MetaRNN

Benign

0.0015

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.24

N;.

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.26

PROVEAN

Benign

0.29

N;N

REVEL

Benign

0.16

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.029

B;B

Vest4

0.023

MPC

0.092

ClinPred

0.00071

GERP RS

-0.44

Varity_R

0.055

gMVP

0.14

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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