NM_015061.6:c.2259+10787G>A

Variant names:

• chr9-7026716-G-A
• rs10975990
• NM_015061.6:c.2259+10787G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015061.6(KDM4C):​c.2259+10787G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,684 control chromosomes in the GnomAD database, including 21,202 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 0.52 (21202 hom., cov: 30)
• Consequence: KDM4C NM_015061.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015061.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM4C	NM_015061.6	MANE Select	c.2259+10787G>A		intron	N/A	NP_055876.2
	KDM4C	NM_001353997.3		c.2259+10787G>A		intron	N/A	NP_001340926.1
	KDM4C	NM_001304339.4		c.2259+10787G>A		intron	N/A	NP_001291268.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM4C	ENST00000381309.8	TSL:1 MANE Select	c.2259+10787G>A		intron	N/A	ENSP00000370710.3
	KDM4C	ENST00000536108.7	TSL:1	c.2259+10787G>A		intron	N/A	ENSP00000440656.4
	KDM4C	ENST00000381306.7	TSL:2	c.2259+10787G>A		intron	N/A	ENSP00000370707.3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79524 AN: 151566 Hom.: 21159 Cov.: 30

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.525 AC: 79632 AN: 151684 Hom.: 21202 Cov.: 30 AF XY: 0.528 AC XY: 39143 AN XY: 74126

African (AFR) AF: 0.590 AC: 24360 AN: 41314

American (AMR) AF: 0.524 AC: 7986 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3468

East Asian (EAS) AF: 0.548 AC: 2809 AN: 5122

South Asian (SAS) AF: 0.699 AC: 3365 AN: 4812

European-Finnish (FIN) AF: 0.483 AC: 5064 AN: 10490

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33032 AN: 67912

Other (OTH) AF: 0.517 AC: 1092 AN: 2114

Alfa AF: 0.505 Hom.: 12118

Bravo AF: 0.524

Asia WGS AF: 0.641 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.21
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10975990; hg19: chr9-7026716;