rs2770304

Variant names:

• chr13-46881230-C-T
• rs2770304
• NM_000621.5:c.613+11160G>A

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+11160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,062 control chromosomes in the GnomAD database, including 31,727 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 0.64 (31727 hom., cov: 32)
• Consequence: HTR2A NM_000621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 27 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR2A	NM_000621.5	MANE Select	c.613+11160G>A		intron	N/A	NP_000612.1
	HTR2A	NM_001378924.1		c.613+11160G>A		intron	N/A	NP_001365853.1
	HTR2A	NM_001165947.5		c.124+11160G>A		intron	N/A	NP_001159419.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR2A	ENST00000542664.4	TSL:1 MANE Select	c.613+11160G>A		intron	N/A	ENSP00000437737.1
	HTR2A	ENST00000543956.5	TSL:1	c.124+11160G>A		intron	N/A	ENSP00000441861.2

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97974 AN: 151942 Hom.: 31704 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.645 AC: 98048 AN: 152062 Hom.: 31727 Cov.: 32 AF XY: 0.643 AC XY: 47795 AN XY: 74316

African (AFR) AF: 0.600 AC: 24892 AN: 41508

American (AMR) AF: 0.638 AC: 9748 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2434 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3511 AN: 5158

South Asian (SAS) AF: 0.655 AC: 3147 AN: 4808

European-Finnish (FIN) AF: 0.635 AC: 6708 AN: 10562

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45419 AN: 67958

Other (OTH) AF: 0.652 AC: 1375 AN: 2110

Alfa AF: 0.661 Hom.: 22408

Bravo AF: 0.639

Asia WGS AF: 0.658 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.78
PhyloP100		-0.32
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: rs2770304; hg19: chr13-47455365;