1-23019614-GGCGGCAGCCGCGGCGGCGGCGGCTGCA-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The ENST00000400181.9(KDM1A):βc.27_53delβ(p.Ala10_Ala18del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000365 in 1,426,404 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Benign (β ). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Likely benign.
Frequency
Consequence
ENST00000400181.9 inframe_deletion
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM1A | NM_001009999.3 | c.27_53del | p.Ala10_Ala18del | inframe_deletion | 1/21 | ENST00000400181.9 | NP_001009999.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDM1A | ENST00000400181.9 | c.27_53del | p.Ala10_Ala18del | inframe_deletion | 1/21 | 1 | NM_001009999.3 | ENSP00000383042 |
Frequencies
GnomAD3 genomes AF: 0.000809 AC: 123AN: 152090Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 76AN: 72596Hom.: 2 AF XY: 0.000733 AC XY: 31AN XY: 42298
GnomAD4 exome AF: 0.000311 AC: 396AN: 1274206Hom.: 3 AF XY: 0.000303 AC XY: 190AN XY: 627324
GnomAD4 genome AF: 0.000815 AC: 124AN: 152198Hom.: 1 Cov.: 32 AF XY: 0.000806 AC XY: 60AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at