dbSNP rs6807670: HTR3C:c.*158G>A (chr3-184060510-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.*158G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 927,970 control chromosomes in the GnomAD database, including 180,257 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 0.61 ( 28462 hom., cov: 31)

Exomes 𝑓: 0.62 ( 151795 hom. )

Consequence

HTR3C
NM_130770.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.846

Publications

14 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:

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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 (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130770.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3C	NM_130770.3	MANE Select	c.*158G>A		3_prime_UTR	Exon 9 of 9	NP_570126.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3C	ENST00000318351.2	TSL:1 MANE Select	c.*158G>A		3_prime_UTR	Exon 9 of 9	ENSP00000322617.1	Q8WXA8

Frequencies

GnomAD3 genomes

AF:

0.609

AC:

92425

AN:

151758

Hom.:

28456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.673

Gnomad ASJ

AF:

0.726

Gnomad EAS

AF:

0.751

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.681

Gnomad MID

AF:

0.621

Gnomad NFE

AF:

0.618

Gnomad OTH

AF:

0.622

GnomAD4 exome

AF:

0.623

AC:

483296

AN:

776094

Hom.:

151795

Cov.:

AF XY:

0.620

AC XY:

246842

AN XY:

397950

show subpopulations

African (AFR)

AF:

0.527

AC:

10273

AN:

19506

American (AMR)

AF:

0.724

AC:

22146

AN:

30600

Ashkenazi Jewish (ASJ)

AF:

0.714

AC:

12324

AN:

17264

East Asian (EAS)

AF:

0.756

AC:

25701

AN:

33986

South Asian (SAS)

AF:

0.561

AC:

33333

AN:

59406

European-Finnish (FIN)

AF:

0.673

AC:

24785

AN:

36854

Middle Eastern (MID)

AF:

0.688

AC:

2935

AN:

4268

European-Non Finnish (NFE)

AF:

0.611

AC:

328098

AN:

536946

Other (OTH)

AF:

0.636

AC:

23701

AN:

37264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

9383

18767

28150

37534

46917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6300

12600

18900

25200

31500

<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:

0.609

AC:

92455

AN:

151876

Hom.:

28462

Cov.:

AF XY:

0.613

AC XY:

45473

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.527

AC:

21833

AN:

41404

American (AMR)

AF:

0.673

AC:

10280

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.726

AC:

2518

AN:

3468

East Asian (EAS)

AF:

0.751

AC:

3868

AN:

5148

South Asian (SAS)

AF:

0.553

AC:

2659

AN:

4808

European-Finnish (FIN)

AF:

0.681

AC:

7185

AN:

10544

Middle Eastern (MID)

AF:

0.620

AC:

181

AN:

292

European-Non Finnish (NFE)

AF:

0.618

AC:

41999

AN:

67928

Other (OTH)

AF:

0.625

AC:

1319

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1784

3567

5351

7134

8918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.619

Hom.:

76001

Bravo

AF:

0.610

Asia WGS

AF:

0.679

AC:

2360

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

1.1

(source)

DANN

Benign

0.56

PhyloP100

0.85

Mutation Taster

=100/0

polymorphism (auto)

(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