rs1328677

chr13-46867375-A-Cchr13-46867375-A-Gchr13-46867375-A-T

Variant summary

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

The NM_000621.5(HTR2A):c.613+25015T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,070 control chromosomes in the GnomAD database, including 33,092 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 0.65 (33092 hom., cov: 32)
• Consequence: HTR2A NM_000621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR2A	NM_000621.5	c.613+25015T>G		intron_variant		ENST00000542664.4
HTR2A	NM_001165947.5	c.124+25015T>G		intron_variant
HTR2A	NM_001378924.1	c.613+25015T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR2A	ENST00000542664.4	c.613+25015T>G		intron_variant		1	NM_000621.5	P1
HTR2A	ENST00000543956.5	c.124+25015T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98845 AN: 151952 Hom.: 33082 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.650 AC: 98902 AN: 152070 Hom.: 33092 Cov.: 32 AF XY: 0.655 AC XY: 48714 AN XY: 74346

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.677

Alfa AF: 0.632 Hom.: 4561

Bravo AF: 0.642

Asia WGS AF: 0.850 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.85
Dann	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1328677; hg19: chr13-47441510;