Variant 5-138372745-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_016604.4(KDM3B):c.264C>T(p.Ile88Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,613,182 control chromosomes in the GnomAD database, including 295,697 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.60 ( 27408 hom., cov: 31)

Exomes 𝑓: 0.60 ( 268289 hom. )

Consequence

KDM3B
NM_016604.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.224

Variant links:

Genes affected

KDM3B (HGNC:1337): (lysine demethylase 3B) Predicted to enable chromatin DNA binding activity; histone H3-methyl-lysine-9 demethylase activity; and transcription coregulator activity. Predicted to be involved in histone H3-K9 demethylation and regulation of transcription by RNA polymerase II. Located in nucleoplasm. Biomarker of acute lymphoblastic leukemia; breast cancer; colorectal cancer; and lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

KDM3B links:

KDM3B (HGNC:):

KDM3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 5-138372745-C-T is Benign according to our data. Variant chr5-138372745-C-T is described in ClinVar as [Benign]. Clinvar id is 1227741.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.224 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDM3B	NM_016604.4 linkuse as main transcript	c.264C>T	p.Ile88Ile	synonymous_variant	2/24	ENST00000314358.10	NP_057688.3	Q7LBC6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KDM3B	ENST00000314358.10 linkuse as main transcript	c.264C>T	p.Ile88Ile	synonymous_variant	2/24	1	NM_016604.4	ENSP00000326563.5	Q7LBC6-1
KDM3B	ENST00000510866.5 linkuse as main transcript	n.72C>T		non_coding_transcript_exon_variant	1/24	1		ENSP00000425186.1	H0Y9V5
KDM3B	ENST00000512928.1 linkuse as main transcript	n.-48C>T		upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90577

AN:

151764

Hom.:

27387

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.629

Gnomad EAS

AF:

0.850

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.592

GnomAD3 exomes

AF:

0.639

AC:

160465

AN:

251302

Hom.:

52403

AF XY:

0.639

AC XY:

86791

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.566

Gnomad AMR exome

AF:

0.730

Gnomad ASJ exome

AF:

0.626

Gnomad EAS exome

AF:

0.853

Gnomad SAS exome

AF:

0.720

Gnomad FIN exome

AF:

0.539

Gnomad NFE exome

AF:

0.585

Gnomad OTH exome

AF:

0.619

GnomAD4 exome

AF:

0.602

AC:

879704

AN:

1461300

Hom.:

268289

Cov.:

AF XY:

0.605

AC XY:

440010

AN XY:

726948

show subpopulations

Gnomad4 AFR exome

AF:

0.571

Gnomad4 AMR exome

AF:

0.724

Gnomad4 ASJ exome

AF:

0.629

Gnomad4 EAS exome

AF:

0.853

Gnomad4 SAS exome

AF:

0.719

Gnomad4 FIN exome

AF:

0.540

Gnomad4 NFE exome

AF:

0.582

Gnomad4 OTH exome

AF:

0.608

GnomAD4 genome

AF:

0.597

AC:

90646

AN:

151882

Hom.:

27408

Cov.:

AF XY:

0.601

AC XY:

44640

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.564

Gnomad4 AMR

AF:

0.660

Gnomad4 ASJ

AF:

0.629

Gnomad4 EAS

AF:

0.849

Gnomad4 SAS

AF:

0.725

Gnomad4 FIN

AF:

0.533

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.595

Alfa

AF:

0.591

Hom.:

35252

Bravo

AF:

0.605

Asia WGS

AF:

0.766

AC:

2663

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

KDM3B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 29, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Diets-Jongmans syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over