dbSNP rs12288145: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR3B	NM_006028.5 link	c.907+118G>A		intron_variant	Intron 7 of 8	ENST00000260191.8	NP_006019.1	O95264-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HTR3B	ENST00000260191.8 link	c.907+118G>A	intron_variant	Intron 7 of 8	1	NM_006028.5	ENSP00000260191.2	O95264-1
HTR3B	ENST00000537778.5 link	c.874+118G>A	intron_variant	Intron 6 of 7	1		ENSP00000443118.1	O95264-2
HTR3B	ENST00000543092.1 link	c.481-1263G>A	intron_variant	Intron 4 of 4	3		ENSP00000440894.1	H0YFX8

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over