rs17420046

chr6-18192322-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364614.2(KDM1B):c.969+941G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 152,190 control chromosomes in the GnomAD database, including 780 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 0.088 (780 hom., cov: 32)
• Consequence: KDM1B NM_001364614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

KDM1B (HGNC:21577): (lysine demethylase 1B) Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KDM1B	NM_001364614.2	c.969+941G>T		intron_variant		ENST00000650836.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KDM1B	ENST00000650836.2	c.969+941G>T		intron_variant			NM_001364614.2	P4
KDM1B	ENST00000546309.6	c.-18-22685G>T		intron_variant		1
KDM1B	ENST00000297792.9	c.574-4735G>T		intron_variant		2
KDM1B	ENST00000449850.2	c.969+941G>T		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13318 AN: 152072 Hom.: 779 Cov.: 32

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0998

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

GnomAD4 genome AF: 0.0875 AC: 13321 AN: 152190 Hom.: 780 Cov.: 32 AF XY: 0.0869 AC XY: 6464 AN XY: 74390

Gnomad4 AFR AF: 0.0208

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0983

Alfa AF: 0.0979 Hom.: 279

Bravo AF: 0.0808

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.4
Dann	Benign	0.61

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

Other links and lift over

dbSNP: rs17420046; hg19: chr6-18192553;