NM_004653.5:c.*94T>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004653.5(KDM5D):c.*94T>C 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.57 ( 0 hom., 17970 hem., cov: 0)
Exomes 𝑓: 0.48 ( 0 hom. 73785 hem. )
Failed GnomAD Quality Control
Consequence
KDM5D
NM_004653.5 3_prime_UTR
NM_004653.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.02
Publications
16 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM5D | NM_004653.5 | c.*94T>C | 3_prime_UTR_variant | Exon 27 of 27 | ENST00000317961.9 | NP_004644.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.565 AC: 17913AN: 31713Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
17913
AN:
31713
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.480 AC: 73785AN: 153686Hom.: 0 Cov.: 0 AF XY: 0.480 AC XY: 73785AN XY: 153686 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
AF:
AC:
73785
AN:
153686
Hom.:
Cov.:
0
AF XY:
AC XY:
73785
AN XY:
153686
show subpopulations
African (AFR)
AF:
AC:
2805
AN:
3394
American (AMR)
AF:
AC:
1722
AN:
4777
Ashkenazi Jewish (ASJ)
AF:
AC:
3072
AN:
4117
East Asian (EAS)
AF:
AC:
7822
AN:
7898
South Asian (SAS)
AF:
AC:
9779
AN:
19499
European-Finnish (FIN)
AF:
AC:
8283
AN:
9102
Middle Eastern (MID)
AF:
AC:
642
AN:
766
European-Non Finnish (NFE)
AF:
AC:
35795
AN:
96744
Other (OTH)
AF:
AC:
3865
AN:
7389
Age Distribution
Exome Hom
Variant carriers
0
704
1408
2112
2816
3520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.566 AC: 17970AN: 31773Hom.: 0 Cov.: 0 AF XY: 0.566 AC XY: 17970AN XY: 31773 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
17970
AN:
31773
Hom.:
Cov.:
0
AF XY:
AC XY:
17970
AN XY:
31773
show subpopulations
African (AFR)
AF:
AC:
6308
AN:
8015
American (AMR)
AF:
AC:
1339
AN:
3536
Ashkenazi Jewish (ASJ)
AF:
AC:
574
AN:
743
East Asian (EAS)
AF:
AC:
1167
AN:
1189
South Asian (SAS)
AF:
AC:
685
AN:
1359
European-Finnish (FIN)
AF:
AC:
2817
AN:
3029
Middle Eastern (MID)
AF:
AC:
70
AN:
73
European-Non Finnish (NFE)
AF:
AC:
4718
AN:
13186
Other (OTH)
AF:
AC:
238
AN:
434
Age Distribution
Genome Hom
Variant carriers
0
236
472
708
944
1180
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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