Variant 2-86456416-ATT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_018433.6(KDM3A):c.557-5_557-4del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 1,044,710 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.000081 ( 0 hom., cov: 0)

Exomes 𝑓: 0.015 ( 0 hom. )

Consequence

KDM3A
NM_018433.6 intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.593

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 -9 ACMG points.

BP6

Variant 2-86456416-ATT-A is Benign according to our data. Variant chr2-86456416-ATT-A is described in ClinVar as [Benign]. Clinvar id is 3038781.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0154 (14132/920540) while in subpopulation SAS AF= 0.0289 (1232/42692). AF 95% confidence interval is 0.0275. There are 0 homozygotes in gnomad4_exome. There are 7218 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High AC in GnomAd4 at 10 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDM3A	NM_018433.6 linkuse as main transcript	c.557-5_557-4del		intron_variant		ENST00000312912.10	NP_060903.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KDM3A	ENST00000312912.10 linkuse as main transcript	c.557-5_557-4del		intron_variant		1	NM_018433.6	ENSP00000323659	P1

Frequencies

GnomAD3 genomes

AF:

0.0000805

AC:

AN:

124186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000838

Gnomad ASJ

AF:

0.000312

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000665

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000818

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0266

AC:

827

AN:

31146

Hom.:

AF XY:

0.0285

AC XY:

494

AN XY:

17322

show subpopulations

Gnomad AFR exome

AF:

0.0227

Gnomad AMR exome

AF:

0.0428

Gnomad ASJ exome

AF:

0.0336

Gnomad EAS exome

AF:

0.0160

Gnomad SAS exome

AF:

0.0504

Gnomad FIN exome

AF:

0.00605

Gnomad NFE exome

AF:

0.0271

Gnomad OTH exome

AF:

0.0370

GnomAD4 exome

AF:

0.0154

AC:

14132

AN:

920540

Hom.:

AF XY:

0.0159

AC XY:

7218

AN XY:

455286

show subpopulations

Gnomad4 AFR exome

AF:

0.0148

Gnomad4 AMR exome

AF:

0.0272

Gnomad4 ASJ exome

AF:

0.0206

Gnomad4 EAS exome

AF:

0.00993

Gnomad4 SAS exome

AF:

0.0289

Gnomad4 FIN exome

AF:

0.0142

Gnomad4 NFE exome

AF:

0.0144

Gnomad4 OTH exome

AF:

0.0167

GnomAD4 genome

AF:

0.0000805

AC:

AN:

124170

Hom.:

Cov.:

AF XY:

0.0000687

AC XY:

AN XY:

58212

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000837

Gnomad4 ASJ

AF:

0.000312

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000665

Gnomad4 NFE

AF:

0.0000818

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

KDM3A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 26, 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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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