chrX-114906591-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000868.4(HTR2C):c.553G>A(p.Val185Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,182,245 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000868.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.553G>A | p.Val185Ile | missense_variant, splice_region_variant | 6/6 | ENST00000276198.6 | |
HTR2C | NM_001256760.3 | c.553G>A | p.Val185Ile | missense_variant, splice_region_variant | 7/7 | ||
HTR2C | NM_001256761.3 | c.458G>A | p.Cys153Tyr | missense_variant, splice_region_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.553G>A | p.Val185Ile | missense_variant, splice_region_variant | 6/6 | 1 | NM_000868.4 | P1 | |
HTR2C | ENST00000371951.5 | c.553G>A | p.Val185Ile | missense_variant, splice_region_variant | 7/7 | 1 | P1 | ||
HTR2C | ENST00000371950.3 | c.458G>A | p.Cys153Tyr | missense_variant, splice_region_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111694Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33886
GnomAD3 exomes AF: 0.0000666 AC: 11AN: 165109Hom.: 0 AF XY: 0.0000560 AC XY: 3AN XY: 53601
GnomAD4 exome AF: 0.0000392 AC: 42AN: 1070551Hom.: 0 Cov.: 27 AF XY: 0.0000439 AC XY: 15AN XY: 341433
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111694Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33886
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.553G>A (p.V185I) alteration is located in exon 6 (coding exon 4) of the HTR2C gene. This alteration results from a G to A substitution at nucleotide position 553, causing the valine (V) at amino acid position 185 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at