2-86456416-A-ATTT

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_018433.6(KDM3A):​c.557-6_557-4dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0061 ( 1 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6
Variant 2-86456416-A-ATTT is Benign according to our data. Variant chr2-86456416-A-ATTT is described in ClinVar as [Benign]. Clinvar id is 3049186.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 25 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KDM3ANM_018433.6 linkuse as main transcriptc.557-6_557-4dup intron_variant ENST00000312912.10 NP_060903.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KDM3AENST00000312912.10 linkuse as main transcriptc.557-6_557-4dup intron_variant 1 NM_018433.6 ENSP00000323659 P1

Frequencies

GnomAD3 genomes
AF:
0.000201
AC:
25
AN:
124184
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000154
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000168
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000222
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000262
Gnomad OTH
AF:
0.000606
GnomAD3 exomes
AF:
0.0176
AC:
547
AN:
31146
Hom.:
2
AF XY:
0.0182
AC XY:
315
AN XY:
17322
show subpopulations
Gnomad AFR exome
AF:
0.0235
Gnomad AMR exome
AF:
0.0181
Gnomad ASJ exome
AF:
0.0162
Gnomad EAS exome
AF:
0.0300
Gnomad SAS exome
AF:
0.0123
Gnomad FIN exome
AF:
0.0208
Gnomad NFE exome
AF:
0.0158
Gnomad OTH exome
AF:
0.0154
GnomAD4 exome
AF:
0.00606
AC:
5625
AN:
927632
Hom.:
1
Cov.:
0
AF XY:
0.00630
AC XY:
2894
AN XY:
459132
show subpopulations
Gnomad4 AFR exome
AF:
0.00770
Gnomad4 AMR exome
AF:
0.00829
Gnomad4 ASJ exome
AF:
0.00887
Gnomad4 EAS exome
AF:
0.00540
Gnomad4 SAS exome
AF:
0.0130
Gnomad4 FIN exome
AF:
0.0121
Gnomad4 NFE exome
AF:
0.00521
Gnomad4 OTH exome
AF:
0.00710
GnomAD4 genome
AF:
0.000201
AC:
25
AN:
124168
Hom.:
0
Cov.:
0
AF XY:
0.000172
AC XY:
10
AN XY:
58218
show subpopulations
Gnomad4 AFR
AF:
0.000154
Gnomad4 AMR
AF:
0.000167
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000222
Gnomad4 NFE
AF:
0.000262
Gnomad4 OTH
AF:
0.000605

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 providedclinical testingPreventionGenetics, part of Exact SciencesNov 25, 2019This 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

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.

Other links and lift over

dbSNP: rs11431031; hg19: chr2-86683539; API