13-46890902-G-T

Position:

• chr13-46890902-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000542664.4(HTR2A):​c.613+1488C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,190 control chromosomes in the GnomAD database, including 2,131 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 0.15 (2131 hom., cov: 32)
• Consequence: HTR2A ENST00000542664.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR2A	NM_000621.5	c.613+1488C>A		intron_variant		ENST00000542664.4	NP_000612.1
HTR2A	NM_001165947.5	c.124+1488C>A		intron_variant			NP_001159419.2
HTR2A	NM_001378924.1	c.613+1488C>A		intron_variant			NP_001365853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR2A	ENST00000542664.4	c.613+1488C>A		intron_variant		1	NM_000621.5	ENSP00000437737	P1
HTR2A	ENST00000543956.5	c.124+1488C>A		intron_variant		1		ENSP00000441861

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22430 AN: 152072 Hom.: 2132 Cov.: 32

Gnomad AFR AF: 0.0354

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22430 AN: 152190 Hom.: 2131 Cov.: 32 AF XY: 0.150 AC XY: 11170 AN XY: 74404

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0897

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.139

Alfa AF: 0.175 Hom.: 3182

Bravo AF: 0.137

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.76

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

Other links and lift over

dbSNP: rs12584920; hg19: chr13-47465037;