13-46872712-C-T

Variant summary

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

The NM_000621.5(HTR2A):​c.613+19678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,988 control chromosomes in the GnomAD database, including 41,572 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 0.74 ( 41572 hom., cov: 30)

Consequence

HTR2A
NM_000621.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.741
Variant links:
Genes affected
HTR2A (HGNC:5293): (5-hydroxytryptamine receptor 2A) This gene encodes one of the receptors for serotonin, a neurotransmitter with many roles. Mutations in this gene are associated with susceptibility to schizophrenia and obsessive-compulsive disorder, and are also associated with response to the antidepressant citalopram in patients with major depressive disorder (MDD). MDD patients who also have a mutation in intron 2 of this gene show a significantly reduced response to citalopram as this antidepressant downregulates expression of this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

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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 (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HTR2ANM_000621.5 linkc.613+19678G>A intron_variant ENST00000542664.4 NP_000612.1 P28223-1
HTR2ANM_001378924.1 linkc.613+19678G>A intron_variant NP_001365853.1
HTR2ANM_001165947.5 linkc.124+19678G>A intron_variant NP_001159419.2 P28223

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HTR2AENST00000542664.4 linkc.613+19678G>A intron_variant 1 NM_000621.5 ENSP00000437737.1 P28223-1
HTR2AENST00000543956.5 linkc.124+19678G>A intron_variant 1 ENSP00000441861.2 A0A7P0PKG8

Frequencies

GnomAD3 genomes
AF:
0.738
AC:
112097
AN:
151872
Hom.:
41546
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.806
Gnomad AMI
AF:
0.864
Gnomad AMR
AF:
0.755
Gnomad ASJ
AF:
0.756
Gnomad EAS
AF:
0.752
Gnomad SAS
AF:
0.632
Gnomad FIN
AF:
0.716
Gnomad MID
AF:
0.712
Gnomad NFE
AF:
0.700
Gnomad OTH
AF:
0.734
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.738
AC:
112173
AN:
151988
Hom.:
41572
Cov.:
30
AF XY:
0.737
AC XY:
54776
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.806
Gnomad4 AMR
AF:
0.755
Gnomad4 ASJ
AF:
0.756
Gnomad4 EAS
AF:
0.752
Gnomad4 SAS
AF:
0.633
Gnomad4 FIN
AF:
0.716
Gnomad4 NFE
AF:
0.700
Gnomad4 OTH
AF:
0.731
Alfa
AF:
0.712
Hom.:
19645
Bravo
AF:
0.744
Asia WGS
AF:
0.669
AC:
2323
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.32
DANN
Benign
0.38

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2770298; hg19: chr13-47446847; API