NM_004653.5:c.*94T>C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

16 publications found
Variant links:
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]

Genome browser will be placed here

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
KDM5DNM_004653.5 linkc.*94T>C 3_prime_UTR_variant Exon 27 of 27 ENST00000317961.9 NP_004644.2 Q9BY66-1A0A384MR42

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KDM5DENST00000317961.9 linkc.*94T>C 3_prime_UTR_variant Exon 27 of 27 1 NM_004653.5 ENSP00000322408.4 Q9BY66-1

Frequencies

GnomAD3 genomes
AF:
0.565
AC:
17913
AN:
31713
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.786
Gnomad AMI
AF:
0.258
Gnomad AMR
AF:
0.380
Gnomad ASJ
AF:
0.773
Gnomad EAS
AF:
0.982
Gnomad SAS
AF:
0.504
Gnomad FIN
AF:
0.930
Gnomad MID
AF:
0.960
Gnomad NFE
AF:
0.358
Gnomad OTH
AF:
0.541
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
AF:
0.480
AC:
73785
AN:
153686
Hom.:
0
Cov.:
0
AF XY:
0.480
AC XY:
73785
AN XY:
153686
show subpopulations
African (AFR)
AF:
0.826
AC:
2805
AN:
3394
American (AMR)
AF:
0.360
AC:
1722
AN:
4777
Ashkenazi Jewish (ASJ)
AF:
0.746
AC:
3072
AN:
4117
East Asian (EAS)
AF:
0.990
AC:
7822
AN:
7898
South Asian (SAS)
AF:
0.502
AC:
9779
AN:
19499
European-Finnish (FIN)
AF:
0.910
AC:
8283
AN:
9102
Middle Eastern (MID)
AF:
0.838
AC:
642
AN:
766
European-Non Finnish (NFE)
AF:
0.370
AC:
35795
AN:
96744
Other (OTH)
AF:
0.523
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:
17970
AN:
31773
Hom.:
0
Cov.:
0
AF XY:
0.566
AC XY:
17970
AN XY:
31773
show subpopulations
African (AFR)
AF:
0.787
AC:
6308
AN:
8015
American (AMR)
AF:
0.379
AC:
1339
AN:
3536
Ashkenazi Jewish (ASJ)
AF:
0.773
AC:
574
AN:
743
East Asian (EAS)
AF:
0.981
AC:
1167
AN:
1189
South Asian (SAS)
AF:
0.504
AC:
685
AN:
1359
European-Finnish (FIN)
AF:
0.930
AC:
2817
AN:
3029
Middle Eastern (MID)
AF:
0.959
AC:
70
AN:
73
European-Non Finnish (NFE)
AF:
0.358
AC:
4718
AN:
13186
Other (OTH)
AF:
0.548
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:
0.436
Hom.:
18660

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.67
DANN
Benign
0.13
PhyloP100
-1.0
Mutation Taster
=100/0
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2032631; hg19: chrY-21867787; API