rs214590

Positions:

• chr6-18209351-C-T

Variant summary

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

The NM_001364614.2(KDM1B):​c.1866+1145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,076 control chromosomes in the GnomAD database, including 12,765 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 0.40 (12765 hom., cov: 32)
• Consequence: KDM1B NM_001364614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDM1B	NM_001364614.2	c.1866+1145C>T		intron_variant		ENST00000650836.2	NP_001351543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KDM1B	ENST00000650836.2	c.1866+1145C>T		intron_variant			NM_001364614.2	ENSP00000499208.1
KDM1B	ENST00000546309.6	c.-18-5656C>T		intron_variant		1		ENSP00000442670.1
KDM1B	ENST00000449850.2	c.1869+1145C>T		intron_variant		5		ENSP00000405669.2
KDM1B	ENST00000297792.9	c.1170+1145C>T		intron_variant		2		ENSP00000297792.5

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60825 AN: 151956 Hom.: 12754 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.400 AC: 60861 AN: 152076 Hom.: 12765 Cov.: 32 AF XY: 0.406 AC XY: 30177 AN XY: 74338

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.418

Alfa AF: 0.426 Hom.: 19362

Bravo AF: 0.390

Asia WGS AF: 0.450 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.39

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: rs214590; hg19: chr6-18209582;