Variant rs757647 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016604.4(KDM3B):c.193-1048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,846 control chromosomes in the GnomAD database, including 7,475 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 0.30 ( 7475 hom., cov: 31)

Consequence

KDM3B
NM_016604.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.755

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 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.193-1048G>A		intron_variant		ENST00000314358.10	NP_057688.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KDM3B	ENST00000314358.10 linkuse as main transcript	c.193-1048G>A		intron_variant		1	NM_016604.4	ENSP00000326563	P1	Q7LBC6-1

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

44999

AN:

151728

Hom.:

7465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.410

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.567

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.333

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.298

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

GnomAD4 genome

AF:

0.297

AC:

45041

AN:

151846

Hom.:

7475

Cov.:

AF XY:

0.302

AC XY:

22412

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.410

Gnomad4 AMR

AF:

0.288

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.568

Gnomad4 SAS

AF:

0.293

Gnomad4 FIN

AF:

0.234

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.242

Hom.:

8554

Bravo

AF:

0.310

Asia WGS

AF:

0.446

AC:

1551

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.7

DANN

Benign

0.43

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over