rs45442400
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004187.5(KDM5C):c.3441C>T(p.Ile1147=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,207,651 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts 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 Likely benign (★★).
Frequency
Consequence
NM_004187.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM5C | NM_004187.5 | c.3441C>T | p.Ile1147= | splice_region_variant, synonymous_variant | 23/26 | ENST00000375401.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM5C | ENST00000375401.8 | c.3441C>T | p.Ile1147= | splice_region_variant, synonymous_variant | 23/26 | 1 | NM_004187.5 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000363 AC: 4AN: 110081Hom.: 0 Cov.: 23 AF XY: 0.0000618 AC XY: 2AN XY: 32373
GnomAD3 exomes AF: 0.0000388 AC: 7AN: 180223Hom.: 0 AF XY: 0.0000455 AC XY: 3AN XY: 65875
GnomAD4 exome AF: 0.000125 AC: 137AN: 1097570Hom.: 0 Cov.: 32 AF XY: 0.000110 AC XY: 40AN XY: 363008
GnomAD4 genome ? AF: 0.0000363 AC: 4AN: 110081Hom.: 0 Cov.: 23 AF XY: 0.0000618 AC XY: 2AN XY: 32373
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital | Dec 07, 2017 | BS2, BP5; This alteration was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and was found in a case with an alternate molecular basis for disease. - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at