6-18216553-C-T

Position:

• chr6-18216553-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.2233-1180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,060 control chromosomes in the GnomAD database, including 6,149 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 0.27 (6149 hom., cov: 32)
• Consequence: KDM1B NM_001364614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KDM1B	NM_001364614.2	c.2233-1180C>T		intron_variant		ENST00000650836.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KDM1B	ENST00000650836.2	c.2233-1180C>T		intron_variant			NM_001364614.2	P4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40975 AN: 151942 Hom.: 6138 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.270 AC: 41019 AN: 152060 Hom.: 6149 Cov.: 32 AF XY: 0.273 AC XY: 20271 AN XY: 74322

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.271

Alfa AF: 0.231 Hom.: 3371

Bravo AF: 0.284

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.72

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: rs214582; hg19: chr6-18216784;