rs6312

Variant names:

• chr13-46896689-C-A
• rs6312
• NM_000621.5:c.-344G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-46896689-C-A
• chr13-46896689-C-G
• chr13-46896689-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000621.5(HTR2A):​c.-344G>T variant causes a 5 prime UTR change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HTR2A NM_000621.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.91

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR2A	NM_000621.5	c.-344G>T		5_prime_UTR_variant	Exon 1 of 4	ENST00000542664.4	NP_000612.1
HTR2A	NM_001165947.5	c.-93G>T		5_prime_UTR_variant	Exon 1 of 3		NP_001159419.2
HTR2A	NM_001378924.1	c.-328-455G>T		intron_variant	Intron 1 of 3		NP_001365853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR2A	ENST00000542664.4	c.-344G>T		5_prime_UTR_variant	Exon 1 of 4	1	NM_000621.5	ENSP00000437737.1
HTR2A	ENST00000543956.5	c.-93G>T		5_prime_UTR_variant	Exon 1 of 3	1		ENSP00000441861.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1380878 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 681346

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.092	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Benign	0.96
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.23
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.050	D
MetaRNN	Uncertain	0.60	D
MetaSVM	Benign	-0.75	T
PROVEAN	Benign	4.3	N
REVEL	Benign	0.15
Sift	Pathogenic	0.0	D
Vest4		0.49
MutPred		0.70		Loss of ubiquitination at K53 (P = 0.1202);
MVP		0.72
ClinPred		0.87	D
GERP RS		4.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6312; hg19: chr13-47470824;