rs6938294

Variant names:

• chr6-18202554-T-C
• rs6938294
• NM_001364614.2:c.1531+897T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364614.2. 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
	KDM1B	NM_001364614.2	MANE Select	c.1531+897T>C		intron	N/A	NP_001351543.1
	KDM1B	NM_001439117.1		c.1558+897T>C		intron	N/A	NP_001426046.1
	KDM1B	NM_001439118.1		c.1558+897T>C		intron	N/A	NP_001426047.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM1B	ENST00000650836.2	MANE Select	c.1531+897T>C		intron	N/A	ENSP00000499208.1
	KDM1B	ENST00000546309.6	TSL:1	c.-18-12453T>C		intron	N/A	ENSP00000442670.1
	KDM1B	ENST00000449850.2	TSL:5	c.1531+897T>C		intron	N/A	ENSP00000405669.2

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

African (AFR) AF: 0.0257 AC: 1067 AN: 41566

American (AMR) AF: 0.0836 AC: 1279 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0722 AC: 348 AN: 4818

European-Finnish (FIN) AF: 0.179 AC: 1897 AN: 10576

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8415 AN: 68004

Other (OTH) AF: 0.100 AC: 212 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.70
DANN	Benign	0.60
PhyloP100		0.0
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: rs6938294; hg19: chr6-18202785;