13-46867572-T-C

Variant names:

• chr13-46867572-T-C
• rs1328674
• NM_000621.5:c.613+24818A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000621.5(HTR2A):​c.613+24818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,290 control chromosomes in the GnomAD database, including 67,449 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 0.94 (67449 hom., cov: 32)
• Consequence: HTR2A NM_000621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000621.5. 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
	HTR2A	NM_000621.5	MANE Select	c.613+24818A>G		intron	N/A	NP_000612.1	P28223-1
	HTR2A	NM_001378924.1		c.613+24818A>G		intron	N/A	NP_001365853.1	P28223-1
	HTR2A	NM_001165947.5		c.124+24818A>G		intron	N/A	NP_001159419.2	A0A7P0PKG8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR2A	ENST00000542664.4	TSL:1 MANE Select	c.613+24818A>G		intron	N/A	ENSP00000437737.1	P28223-1
	HTR2A	ENST00000543956.5	TSL:1	c.124+24818A>G		intron	N/A	ENSP00000441861.2	A0A7P0PKG8
	HTR2A	ENST00000941626.1		c.613+24818A>G		intron	N/A	ENSP00000611685.1

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143187 AN: 152172 Hom.: 67403 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.941 AC: 143293 AN: 152290 Hom.: 67449 Cov.: 32 AF XY: 0.941 AC XY: 70104 AN XY: 74460

African (AFR) AF: 0.900 AC: 37412 AN: 41560

American (AMR) AF: 0.943 AC: 14427 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3308 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5021 AN: 5178

South Asian (SAS) AF: 0.980 AC: 4724 AN: 4822

European-Finnish (FIN) AF: 0.966 AC: 10248 AN: 10612

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65050 AN: 68030

Other (OTH) AF: 0.926 AC: 1960 AN: 2116

Alfa AF: 0.951 Hom.: 203914

Bravo AF: 0.936

Asia WGS AF: 0.970 AC: 3374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.56
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1328674; hg19: chr13-47441707;