Variant rs193921056 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018433.6(KDM3A):c.2685+14_2685+17del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 1,612,470 control chromosomes in the GnomAD database, including 4,896 homozygotes. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.073 ( 439 hom., cov: 31)

Exomes 𝑓: 0.075 ( 4457 hom. )

Consequence

KDM3A
NM_018433.6 splice_donor_region, intron

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.00100

Variant links:

Genes affected

KDM3A (HGNC:20815): (lysine demethylase 3A) Enables androgen receptor binding activity; histone H3-methyl-lysine-9 demethylase activity; and iron ion binding activity. Involved in several processes, including androgen receptor signaling pathway; formaldehyde biosynthetic process; and histone H3-K9 demethylation. Located in nucleoplasm. Implicated in cervical cancer and colon cancer. Biomarker of Ewing sarcoma; hepatocellular carcinoma; nasopharynx carcinoma; and prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

KDM3A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KDM3A	NM_018433.6 linkuse as main transcript	c.2685+14_2685+17del		splice_donor_region_variant, intron_variant		ENST00000312912.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
KDM3A	ENST00000312912.10 linkuse as main transcript	c.2685+14_2685+17del	splice_donor_region_variant, intron_variant	1	NM_018433.6	P1
KDM3A	ENST00000409064.5 linkuse as main transcript	c.2685+14_2685+17del	splice_donor_region_variant, intron_variant	1		P1
KDM3A	ENST00000409556.5 linkuse as main transcript	c.2685+14_2685+17del	splice_donor_region_variant, intron_variant	5		P1
KDM3A	ENST00000441719.5 linkuse as main transcript	c.2120+14_2120+17del	splice_donor_region_variant, intron_variant, NMD_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0726

AC:

11045

AN:

152148

Hom.:

439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0716

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0560

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.00943

Gnomad SAS

AF:

0.0434

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0789

Gnomad OTH

AF:

0.0573

GnomAD3 exomes

AF:

0.0649

AC:

16304

AN:

251078

Hom.:

633

AF XY:

0.0660

AC XY:

8952

AN XY:

135710

show subpopulations

Gnomad AFR exome

AF:

0.0697

Gnomad AMR exome

AF:

0.0360

Gnomad ASJ exome

AF:

0.0304

Gnomad EAS exome

AF:

0.00903

Gnomad SAS exome

AF:

0.0496

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.0786

Gnomad OTH exome

AF:

0.0652

GnomAD4 exome

AF:

0.0751

AC:

109617

AN:

1460204

Hom.:

4457

AF XY:

0.0743

AC XY:

53956

AN XY:

726530

show subpopulations

Gnomad4 AFR exome

AF:

0.0701

Gnomad4 AMR exome

AF:

0.0379

Gnomad4 ASJ exome

AF:

0.0320

Gnomad4 EAS exome

AF:

0.0204

Gnomad4 SAS exome

AF:

0.0504

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.0795

Gnomad4 OTH exome

AF:

0.0721

GnomAD4 genome

AF:

0.0726

AC:

11052

AN:

152266

Hom.:

439

Cov.:

AF XY:

0.0734

AC XY:

5467

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0715

Gnomad4 AMR

AF:

0.0559

Gnomad4 ASJ

AF:

0.0323

Gnomad4 EAS

AF:

0.00984

Gnomad4 SAS

AF:

0.0443

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.0789

Gnomad4 OTH

AF:

0.0572

Alfa

AF:

0.0431

Hom.:

Bravo

AF:

0.0672

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

EpiCase

AF:

0.0757

EpiControl

AF:

0.0771

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Malignant tumor of prostate

Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

Science for Life laboratory, Karolinska Institutet

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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