Variant 9-6784726-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015061.6(KDM4C):c.-17-8246G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,058 control chromosomes in the GnomAD database, including 23,682 homozygotes. 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 0.55 ( 23682 hom., cov: 32)

Consequence

KDM4C
NM_015061.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.575

Variant links:

Genes affected

KDM4C (HGNC:17071): (lysine demethylase 4C) This gene is a member of the Jumonji domain 2 (JMJD2) family. The encoded protein is a trimethylation-specific demethylase, and converts specific trimethylated histone residues to the dimethylated form. This enzymatic action regulates gene expression and chromosome segregation. Chromosomal aberrations and changes in expression of this gene may be found in tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

KDM4C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDM4C	NM_015061.6 link	c.-17-8246G>C		intron_variant		ENST00000381309.8	NP_055876.2	Q9H3R0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KDM4C	ENST00000381309.8 link	c.-17-8246G>C		intron_variant		1	NM_015061.6	ENSP00000370710.3		Q9H3R0-1

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83471

AN:

151938

Hom.:

23643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.703

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.512

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.558

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.550

AC:

83567

AN:

152058

Hom.:

23682

Cov.:

AF XY:

0.545

AC XY:

40462

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.703

Gnomad4 AMR

AF:

0.505

Gnomad4 ASJ

AF:

0.481

Gnomad4 EAS

AF:

0.397

Gnomad4 SAS

AF:

0.513

Gnomad4 FIN

AF:

0.449

Gnomad4 NFE

AF:

0.500

Gnomad4 OTH

AF:

0.554

Alfa

AF:

0.363

Hom.:

838

Bravo

AF:

0.557

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.5

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over