Genetic Variant KDM1B:c.574-107C>T (chr6-18187685-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001364614.2(KDM1B):c.574-107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 725,170 control chromosomes in the GnomAD database, including 246,430 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 0.86 ( 56269 hom., cov: 31)

Exomes 𝑓: 0.81 ( 190161 hom. )

Consequence

KDM1B
NM_001364614.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.923

Publications

4 publications found

Variant links:

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]

KDM1B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KDM1B	NM_001364614.2	MANE Select	c.574-107C>T	intron	N/A	NP_001351543.1	Q8NB78-1
KDM1B	NM_001439117.1		c.601-107C>T	intron	N/A	NP_001426046.1
KDM1B	NM_001439118.1		c.601-107C>T	intron	N/A	NP_001426047.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KDM1B	ENST00000650836.2	MANE Select	c.574-107C>T	intron	N/A	ENSP00000499208.1	Q8NB78-1
KDM1B	ENST00000546309.6	TSL:1	c.-18-27322C>T	intron	N/A	ENSP00000442670.1	Q08EI0
KDM1B	ENST00000449850.2	TSL:5	c.574-107C>T	intron	N/A	ENSP00000405669.2	H0Y6H0

Frequencies

GnomAD3 genomes

AF:

0.856

AC:

130106

AN:

152048

Hom.:

56208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.964

Gnomad AMI

AF:

0.884

Gnomad AMR

AF:

0.888

Gnomad ASJ

AF:

0.829

Gnomad EAS

AF:

0.647

Gnomad SAS

AF:

0.826

Gnomad FIN

AF:

0.798

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.853

GnomAD4 exome

AF:

0.812

AC:

465429

AN:

573004

Hom.:

190161

AF XY:

0.810

AC XY:

242896

AN XY:

299830

show subpopulations

African (AFR)

AF:

0.966

AC:

15390

AN:

15934

American (AMR)

AF:

0.912

AC:

28080

AN:

30784

Ashkenazi Jewish (ASJ)

AF:

0.834

AC:

14195

AN:

17014

East Asian (EAS)

AF:

0.642

AC:

20298

AN:

31640

South Asian (SAS)

AF:

0.825

AC:

45216

AN:

54820

European-Finnish (FIN)

AF:

0.800

AC:

27233

AN:

34024

Middle Eastern (MID)

AF:

0.812

AC:

3105

AN:

3826

European-Non Finnish (NFE)

AF:

0.809

AC:

286770

AN:

354296

Other (OTH)

AF:

0.820

AC:

25142

AN:

30666

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

4281

8562

12843

17124

21405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2706

5412

8118

10824

13530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.856

AC:

130227

AN:

152166

Hom.:

56269

Cov.:

AF XY:

0.854

AC XY:

63498

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.964

AC:

40011

AN:

41518

American (AMR)

AF:

0.888

AC:

13581

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.829

AC:

2877

AN:

3472

East Asian (EAS)

AF:

0.647

AC:

3324

AN:

5140

South Asian (SAS)

AF:

0.827

AC:

3987

AN:

4820

European-Finnish (FIN)

AF:

0.798

AC:

8455

AN:

10594

Middle Eastern (MID)

AF:

0.793

AC:

233

AN:

294

European-Non Finnish (NFE)

AF:

0.811

AC:

55156

AN:

68012

Other (OTH)

AF:

0.850

AC:

1797

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

926

1852

2778

3704

4630

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.843

Hom.:

8572

Bravo

AF:

0.867

Asia WGS

AF:

0.766

AC:

2662

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.35

(source)

DANN

Benign

0.66

PhyloP100

-0.92

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over