chrX-53192606-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004187.5(KDM5C):c.*361C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 20 hom., 324 hem., cov: 20)
Exomes 𝑓: 0.0018 ( 11 hom. 223 hem. )
Consequence
KDM5C
NM_004187.5 3_prime_UTR
NM_004187.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.150
Genes affected
KDM5C (HGNC:11114): (lysine demethylase 5C) This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. 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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant X-53192606-G-T is Benign according to our data. Variant chrX-53192606-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1207328.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0125 (1361/108945) while in subpopulation AFR AF= 0.0431 (1284/29793). AF 95% confidence interval is 0.0411. There are 20 homozygotes in gnomad4. There are 324 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM5C | NM_004187.5 | c.*361C>A | 3_prime_UTR_variant | 26/26 | ENST00000375401.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM5C | ENST00000375401.8 | c.*361C>A | 3_prime_UTR_variant | 26/26 | 1 | NM_004187.5 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.0125 AC: 1358AN: 108896Hom.: 20 Cov.: 20 AF XY: 0.0102 AC XY: 319AN XY: 31204
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GnomAD4 exome AF: 0.00176 AC: 909AN: 515175Hom.: 11 Cov.: 8 AF XY: 0.00163 AC XY: 223AN XY: 136819
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GnomAD4 genome ? AF: 0.0125 AC: 1361AN: 108945Hom.: 20 Cov.: 20 AF XY: 0.0104 AC XY: 324AN XY: 31263
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 27, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
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Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at