chrX-114878807-A-G

Variant names:

• chrX-114878807-A-G
• rs5946018
• NM_000868.4:c.551-27782A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000868.4(HTR2C):​c.551-27782A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.85 (28129 hom., 27177 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: HTR2C NM_000868.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 2 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000868.4. 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
	HTR2C	NM_000868.4	MANE Select	c.551-27782A>G		intron	N/A	NP_000859.2
	HTR2C	NM_001256760.3		c.551-27782A>G		intron	N/A	NP_001243689.2
	HTR2C	NM_001256761.3		c.456-27782A>G		intron	N/A	NP_001243690.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR2C	ENST00000276198.6	TSL:1 MANE Select	c.551-27782A>G		intron	N/A	ENSP00000276198.1
	HTR2C	ENST00000371951.5	TSL:1	c.551-27782A>G		intron	N/A	ENSP00000361019.1
	HTR2C	ENST00000371950.3	TSL:1	c.456-27782A>G		intron	N/A	ENSP00000361018.3

Frequencies

GnomAD3 genomes AF: 0.853 AC: 93056 AN: 109081 Hom.: 28136 Cov.: 22

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.884

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.853 AC: 93094 AN: 109126 Hom.: 28129 Cov.: 22 AF XY: 0.857 AC XY: 27177 AN XY: 31714

African (AFR) AF: 0.823 AC: 24893 AN: 30261

American (AMR) AF: 0.922 AC: 9330 AN: 10119

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2129 AN: 2615

East Asian (EAS) AF: 0.991 AC: 3459 AN: 3492

South Asian (SAS) AF: 0.899 AC: 2352 AN: 2617

European-Finnish (FIN) AF: 0.881 AC: 4911 AN: 5574

Middle Eastern (MID) AF: 0.812 AC: 168 AN: 207

European-Non Finnish (NFE) AF: 0.845 AC: 43995 AN: 52083

Other (OTH) AF: 0.884 AC: 1316 AN: 1489

Alfa AF: 0.749 Hom.: 2753

Bravo AF: 0.856

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.66
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: rs5946018; hg19: chrX-114113370;