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GeneBe

rs3813929

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The X-114584047-C-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 111000 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. There are no hemizygote samples in GnomAD Genomes, and 0 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 0.000018 ( 0 hom., 0 hem., cov: 21)

Consequence

HTR2C
NM_000868.4 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.695

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.000018 (2/111000) while in subpopulation AFR AF= 0.0000653 (2/30644). AF 95% confidence interval is 0.0000108. There are 0 homozygotes in gnomad. There are 0 alleles in male gnomad subpopulation. Median coverage is 21. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTR2CNM_000868.4 linkuse as main transcript upstream_gene_variant ENST00000276198.6
HTR2CNM_001256760.3 linkuse as main transcript upstream_gene_variant
HTR2CNM_001256761.3 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTR2CENST00000276198.6 linkuse as main transcript upstream_gene_variant 1 NM_000868.4 P1P28335-1
HTR2CENST00000371950.3 linkuse as main transcript upstream_gene_variant 1 P28335-2
HTR2CENST00000371951.5 linkuse as main transcript upstream_gene_variant 1 P1P28335-1

Frequencies

GnomAD3 genomes
AF:
0.0000180
AC:
2
AN:
111000
Hom.:
0
Cov.:
21
AF XY:
0.00
AC XY:
0
AN XY:
33222
show subpopulations
Gnomad AFR
AF:
0.0000653
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
Bravo
AF:
0.0000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
Cadd
Benign
3.5
Dann
Benign
0.77

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3813929; hg19: chrX-113818520; API