chr1-23019740-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001009999.3(KDM1A):c.144C>T(p.Ala48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000012 in 1,334,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A48A) has been classified as Likely benign.
Frequency
Consequence
NM_001009999.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM1A | NM_001009999.3 | c.144C>T | p.Ala48= | synonymous_variant | 1/21 | ENST00000400181.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM1A | ENST00000400181.9 | c.144C>T | p.Ala48= | synonymous_variant | 1/21 | 1 | NM_001009999.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151930Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000110 AC: 13AN: 1182516Hom.: 0 Cov.: 31 AF XY: 0.0000123 AC XY: 7AN XY: 569032
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151930Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74208
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | KDM1A: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at