chr16-27203663-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000286096.9(KDM8):​c.-32+27G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 164,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0014 ( 0 hom. )

Consequence

KDM8
ENST00000286096.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.188
Variant links:
Genes affected
KDM8 (HGNC:25840): (lysine demethylase 8) This gene likely encodes a histone lysine demethylase. Studies of a similar protein in mouse indicate a potential role for this protein as a tumor suppressor. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KDM8NM_024773.3 linkuse as main transcriptc.-32+27G>C intron_variant ENST00000286096.9 NP_079049.2
KDM8XM_017023676.2 linkuse as main transcriptc.-32+27G>C intron_variant XP_016879165.1
KDM8XM_047434654.1 linkuse as main transcriptc.-32+27G>C intron_variant XP_047290610.1
KDM8XM_047434655.1 linkuse as main transcriptc.-32+27G>C intron_variant XP_047290611.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KDM8ENST00000286096.9 linkuse as main transcriptc.-32+27G>C intron_variant 1 NM_024773.3 ENSP00000286096 P1Q8N371-1
KDM8ENST00000564961.1 linkuse as main transcriptn.129+27G>C intron_variant, non_coding_transcript_variant 1
KDM8ENST00000562269.1 linkuse as main transcriptn.120+27G>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00125
AC:
191
AN:
152240
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00103
Gnomad FIN
AF:
0.000564
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00231
Gnomad OTH
AF:
0.00143
GnomAD4 exome
AF:
0.00136
AC:
17
AN:
12482
Hom.:
0
Cov.:
0
AF XY:
0.00131
AC XY:
9
AN XY:
6892
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00105
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00178
Gnomad4 OTH exome
AF:
0.00293
GnomAD4 genome
AF:
0.00125
AC:
191
AN:
152358
Hom.:
0
Cov.:
34
AF XY:
0.00119
AC XY:
89
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.000313
Gnomad4 AMR
AF:
0.000457
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.000564
Gnomad4 NFE
AF:
0.00231
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.0000774
Hom.:
13
Bravo
AF:
0.00129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
0.89
DANN
Benign
0.58

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16976587; hg19: chr16-27214984; API