dbSNP rs6808122: HTR3C:c.234+146G>A (chr3-184055033-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_130770.3(HTR3C):c.234+146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 785,828 control chromosomes in the GnomAD database, including 172,596 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 0.72 ( 39782 hom., cov: 34)

Exomes 𝑓: 0.64 ( 132814 hom. )

Consequence

HTR3C
NM_130770.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.314

Publications

6 publications found

Variant links:

Genes affected

HTR3C (HGNC:24003): (5-hydroxytryptamine receptor 3C) The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit C 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. Genes encoding subunits C, D and E form a cluster on chromosome 3. [provided by RefSeq, Jul 2008]

HTR3C 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR3C	NM_130770.3 link	c.234+146G>A		intron_variant	Intron 2 of 8	ENST00000318351.2	NP_570126.2	Q8WXA8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR3C	ENST00000318351.2 link	c.234+146G>A		intron_variant	Intron 2 of 8	1	NM_130770.3	ENSP00000322617.1		Q8WXA8

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108827

AN:

152044

Hom.:

39732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.859

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.763

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.768

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.671

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.630

Gnomad OTH

AF:

0.715

GnomAD4 exome

AF:

0.642

AC:

406923

AN:

633666

Hom.:

132814

AF XY:

0.639

AC XY:

208149

AN XY:

325564

show subpopulations

African (AFR)

AF:

0.866

AC:

13445

AN:

15530

American (AMR)

AF:

0.789

AC:

14633

AN:

18550

Ashkenazi Jewish (ASJ)

AF:

0.732

AC:

10828

AN:

14788

East Asian (EAS)

AF:

0.738

AC:

23517

AN:

31854

South Asian (SAS)

AF:

0.579

AC:

28170

AN:

48656

European-Finnish (FIN)

AF:

0.669

AC:

23920

AN:

35746

Middle Eastern (MID)

AF:

0.735

AC:

1797

AN:

2444

European-Non Finnish (NFE)

AF:

0.620

AC:

268991

AN:

434062

Other (OTH)

AF:

0.675

AC:

21622

AN:

32036

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

7268

14536

21805

29073

36341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4336

8672

13008

17344

21680

<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:

0.716

AC:

108930

AN:

152162

Hom.:

39782

Cov.:

AF XY:

0.718

AC XY:

53399

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.859

AC:

35661

AN:

41522

American (AMR)

AF:

0.763

AC:

11663

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.748

AC:

2598

AN:

3472

East Asian (EAS)

AF:

0.767

AC:

3972

AN:

5176

South Asian (SAS)

AF:

0.572

AC:

2760

AN:

4826

European-Finnish (FIN)

AF:

0.671

AC:

7104

AN:

10588

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.630

AC:

42836

AN:

67970

Other (OTH)

AF:

0.719

AC:

1520

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1572

3143

4715

6286

7858

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<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:

0.660

Hom.:

24621

Bravo

AF:

0.735

Asia WGS

AF:

0.728

AC:

2532

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.8

(source)

DANN

Benign

0.48

PhyloP100

0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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