X-114584047-C-T

Variant names:

• chrX-114584047-C-T
• rs3813929
• NM_000868.4:c.-759C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000868.4(HTR2C):​c.-759C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 111,327 control chromosomes in the GnomAD database, including 762 homozygotes. There are 4,306 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.13 (761 hom., 4286 hem., cov: 21)
  • Exomes 𝑓: 0.16 (1 hom. 20 hem.)
• Consequence: HTR2C NM_000868.4 upstream_gene
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.695

Genes affected

HTR2C (HGNC:5295): (5-hydroxytryptamine receptor 2C) This gene encodes a seven-transmembrane G-protein-coupled receptor. The encoded protein responds to signaling through the neurotransmitter serotonin. The mRNA of this gene is subject to multiple RNA editing events, where adenosine residues encoded by the genome are converted to inosines. RNA editing is predicted to alter the structure of the second intracellular loop, thereby generating alternate protein forms with decreased ability to interact with G proteins. Abnormalities in RNA editing of this gene have been detected in victims of suicide that suffer from depression. In addition, naturally-occuring variation in the promoter and 5' non-coding and coding regions of this gene may show statistically-significant association with mental illness and behavioral disorders. Alternative splicing results in multiple different transcript variants. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant X-114584047-C-T is Benign according to our data. Variant chrX-114584047-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 225992.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR2C	NM_000868.4	c.-759C>T		upstream_gene_variant		ENST00000276198.6	NP_000859.2
HTR2C	NM_001256760.3	c.-850C>T		upstream_gene_variant			NP_001243689.2
HTR2C	NM_001256761.3	c.-759C>T		upstream_gene_variant			NP_001243690.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR2C	ENST00000276198.6	c.-759C>T		upstream_gene_variant		1	NM_000868.4	ENSP00000276198.1
HTR2C	ENST00000371951.5	c.-850C>T		upstream_gene_variant		1		ENSP00000361019.1
HTR2C	ENST00000371950.3	c.-759C>T		upstream_gene_variant		1		ENSP00000361018.3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 14111 AN: 110991 Hom.: 762 Cov.: 21 AF XY: 0.129 AC XY: 4278 AN XY: 33215

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0294

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.155 AC: 44 AN: 283 Hom.: 1 Cov.: 0 AF XY: 0.180 AC XY: 20 AN XY: 111

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.151

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.127 AC: 14116 AN: 111044 Hom.: 761 Cov.: 21 AF XY: 0.129 AC XY: 4286 AN XY: 33278

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.128

Alfa AF: 0.148 Hom.: 3978

Bravo AF: 0.119

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Aug 14, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 15741483, 17376412, 21391883, 18192901, 19106782, 20010450, 20453482, 10768099) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.0
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813929; hg19: chrX-113818520; COSMIC: COSV52200938;