Y-19727881-A-T

Variant names:

• chrY-19727881-A-T
• rs2032635
• NM_004653.5:c.1371+3891T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004653.5(KDM5D):​c.1371+3891T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
• Consequence: KDM5D NM_004653.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 9 publications found

Genes affected

KDM5D (HGNC:11115): (lysine demethylase 5D) This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004653.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM5D	NM_004653.5	MANE Select	c.1371+3891T>A		intron	N/A	NP_004644.2
	KDM5D	NM_001146705.2		c.1371+3891T>A		intron	N/A	NP_001140177.1	Q9BY66-3
	KDM5D	NM_001146706.2		c.1200+3891T>A		intron	N/A	NP_001140178.1	Q9BY66-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM5D	ENST00000317961.9	TSL:1 MANE Select	c.1371+3891T>A		intron	N/A	ENSP00000322408.4	Q9BY66-1
	KDM5D	ENST00000541639.5	TSL:1	c.1371+3891T>A		intron	N/A	ENSP00000444293.1	Q9BY66-3
	KDM5D	ENST00000382806.6	TSL:1	c.1200+3891T>A		intron	N/A	ENSP00000372256.2	Q9BY66-2

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.13
PhyloP100		-2.0

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

Other links and lift over

dbSNP: rs2032635; hg19: chrY-21889767;