Genetic Variant HTR3B:c.907+118G>A (chr11-113943310-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006028.5(HTR3B):c.907+118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0383 in 807,448 control chromosomes in the GnomAD database, including 709 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 0.033 ( 102 hom., cov: 32)

Exomes 𝑓: 0.040 ( 607 hom. )

Consequence

HTR3B
NM_006028.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.163

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0543 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.907+118G>A		intron	N/A	NP_006019.1
	HTR3B	NM_001363563.2		c.874+118G>A		intron	N/A	NP_001350492.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
HTR3B	ENST00000260191.8	TSL:1 MANE Select	c.907+118G>A	intron	N/A	ENSP00000260191.2
HTR3B	ENST00000537778.5	TSL:1	c.874+118G>A	intron	N/A	ENSP00000443118.1
HTR3B	ENST00000543092.1	TSL:3	c.481-1263G>A	intron	N/A	ENSP00000440894.1

Frequencies

GnomAD3 genomes

AF:

0.0327

AC:

4979

AN:

152070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0214

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.0346

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.000775

Gnomad SAS

AF:

0.0587

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.0400

Gnomad OTH

AF:

0.0435

GnomAD4 exome

AF:

0.0395

AC:

25911

AN:

655260

Hom.:

607

AF XY:

0.0415

AC XY:

14240

AN XY:

343148

show subpopulations

African (AFR)

AF:

0.0198

AC:

346

AN:

17472

American (AMR)

AF:

0.0257

AC:

858

AN:

33346

Ashkenazi Jewish (ASJ)

AF:

0.0737

AC:

1375

AN:

18662

East Asian (EAS)

AF:

0.000249

AC:

AN:

32168

South Asian (SAS)

AF:

0.0644

AC:

3849

AN:

59794

European-Finnish (FIN)

AF:

0.0150

AC:

638

AN:

42620

Middle Eastern (MID)

AF:

0.0675

AC:

172

AN:

2548

European-Non Finnish (NFE)

AF:

0.0415

AC:

17227

AN:

415448

Other (OTH)

AF:

0.0433

AC:

1438

AN:

33202

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1325

2651

3976

5302

6627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

328

656

984

1312

1640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0327

AC:

4984

AN:

152188

Hom.:

102

Cov.:

AF XY:

0.0317

AC XY:

2359

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0214

AC:

890

AN:

41532

American (AMR)

AF:

0.0346

AC:

530

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0709

AC:

246

AN:

3470

East Asian (EAS)

AF:

0.000776

AC:

AN:

5152

South Asian (SAS)

AF:

0.0600

AC:

289

AN:

4816

European-Finnish (FIN)

AF:

0.0141

AC:

150

AN:

10608

Middle Eastern (MID)

AF:

0.0890

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0399

AC:

2716

AN:

67998

Other (OTH)

AF:

0.0430

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

250

501

751

1002

1252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0309

Hom.:

Bravo

AF:

0.0334

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.8

(source)

DANN

Benign

0.21

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over