rs6938294

Positions:

• chr6-18202554-T-C
• chr6-18202554-T-G

Variant summary

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

The NM_001364614.2(KDM1B):​c.1531+897T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,224 control chromosomes in the GnomAD database, including 840 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 0.092 (840 hom., cov: 32)
• Consequence: KDM1B NM_001364614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDM1B	NM_001364614.2	c.1531+897T>C		intron_variant		ENST00000650836.2	NP_001351543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KDM1B	ENST00000650836.2	c.1531+897T>C		intron_variant			NM_001364614.2	ENSP00000499208	P4
KDM1B	ENST00000546309.6	c.-18-12453T>C		intron_variant		1		ENSP00000442670
KDM1B	ENST00000297792.9	c.963+1978T>C		intron_variant		2		ENSP00000297792
KDM1B	ENST00000449850.2	c.1531+897T>C		intron_variant		5		ENSP00000405669	A1

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13920 AN: 152106 Hom.: 836 Cov.: 32

Gnomad AFR AF: 0.0253

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0916 AC: 13937 AN: 152224 Hom.: 840 Cov.: 32 AF XY: 0.0918 AC XY: 6829 AN XY: 74418

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0722

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0484 Hom.: 53

Bravo AF: 0.0835

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.70
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

Other links and lift over

dbSNP: rs6938294; hg19: chr6-18202785;