Y-19732172-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_004653.5(KDM5D):c.1093-7A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0067 ( 0 hom., 217 hem., cov: 0)
Exomes 𝑓: 0.013 ( 0 hom. 4698 hem. )
Consequence
KDM5D
NM_004653.5 splice_region, splice_polypyrimidine_tract, intron
NM_004653.5 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00004107
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.49
Genes affected
KDM5D (HGNC:11115): (lysine demethylase 5D) This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant Y-19732172-T-C is Benign according to our data. Variant chrY-19732172-T-C is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM5D | NM_004653.5 | c.1093-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000317961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM5D | ENST00000317961.9 | c.1093-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004653.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00660 AC: 214AN: 32409Hom.: 0 Cov.: 0 AF XY: 0.00660 AC XY: 214AN XY: 32409
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0265 AC: 1512AN: 57102Hom.: 0 AF XY: 0.0265 AC XY: 1512AN XY: 57102
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GnomAD4 exome AF: 0.0132 AC: 4698AN: 355816Hom.: 0 Cov.: 1 AF XY: 0.0132 AC XY: 4698AN XY: 355816
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GnomAD4 genome ? AF: 0.00668 AC: 217AN: 32473Hom.: 0 Cov.: 0 AF XY: 0.00668 AC XY: 217AN XY: 32473
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at