Variant X-44873369-T-TGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001291415.2(KDM6A):c.-167_-165dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 988 hom., 2867 hem., cov: 18)

Exomes 𝑓: 0.060 ( 755 hom. 7047 hem. )

Consequence

KDM6A
NM_001291415.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.304

Variant links:

Genes affected

KDM6A (HGNC:12637): (lysine demethylase 6A) This gene is located on the X chromosome and is the corresponding locus to a Y-linked gene which encodes a tetratricopeptide repeat (TPR) protein. The encoded protein of this gene contains a JmjC-domain and catalyzes the demethylation of tri/dimethylated histone H3. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]

KDM6A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-44873369-T-TGCC is Benign according to our data. Variant chrX-44873369-T-TGCC is described in ClinVar as [Benign]. Clinvar id is 1221796.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KDM6A	NM_001291415.2 linkuse as main transcript	c.-167_-165dup		5_prime_UTR_variant	1/30	ENST00000611820.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KDM6A	ENST00000611820.5 linkuse as main transcript	c.-167_-165dup		5_prime_UTR_variant	1/30	1	NM_001291415.2	P4

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

12697

AN:

106086

Hom.:

985

Cov.:

AF XY:

0.0958

AC XY:

2859

AN XY:

29848

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.0123

Gnomad AMR

AF:

0.0847

Gnomad ASJ

AF:

0.0583

Gnomad EAS

AF:

0.0426

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0265

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0647

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.0596

AC:

27322

AN:

458727

Hom.:

755

Cov.:

AF XY:

0.0624

AC XY:

7047

AN XY:

112939

show subpopulations

Gnomad4 AFR exome

AF:

0.246

Gnomad4 AMR exome

AF:

0.0569

Gnomad4 ASJ exome

AF:

0.0646

Gnomad4 EAS exome

AF:

0.0266

Gnomad4 SAS exome

AF:

0.0982

Gnomad4 FIN exome

AF:

0.0391

Gnomad4 NFE exome

AF:

0.0535

Gnomad4 OTH exome

AF:

0.0770

GnomAD4 genome

AF:

0.120

AC:

12706

AN:

106118

Hom.:

988

Cov.:

AF XY:

0.0959

AC XY:

2867

AN XY:

29890

show subpopulations

Gnomad4 AFR

AF:

0.264

Gnomad4 AMR

AF:

0.0845

Gnomad4 ASJ

AF:

0.0583

Gnomad4 EAS

AF:

0.0422

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.0265

Gnomad4 NFE

AF:

0.0647

Gnomad4 OTH

AF:

0.111

Asia WGS

AF:

0.0950

AC:

239

AN:

2503

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 2019

- -

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.

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