Y-19728291-G-A

Variant names:

• chrY-19728291-G-A
• rs2032639
• NM_004653.5:c.1371+3481C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004653.5(KDM5D):​c.1371+3481C>T 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: 𝑓 0.0087 (0 hom., 294 hem., cov: 0)
• Consequence: KDM5D NM_004653.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 6 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00869 (294/33822) while in subpopulation AFR AF = 0.0325 (283/8705). AF 95% confidence interval is 0.0294. There are 0 homozygotes in GnomAd4. There are 294 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 294 gene

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+3481C>T		intron	N/A	NP_004644.2
	KDM5D	NM_001146705.2		c.1371+3481C>T		intron	N/A	NP_001140177.1	Q9BY66-3
	KDM5D	NM_001146706.2		c.1200+3481C>T		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+3481C>T		intron	N/A	ENSP00000322408.4	Q9BY66-1
	KDM5D	ENST00000541639.5	TSL:1	c.1371+3481C>T		intron	N/A	ENSP00000444293.1	Q9BY66-3
	KDM5D	ENST00000382806.6	TSL:1	c.1200+3481C>T		intron	N/A	ENSP00000372256.2	Q9BY66-2

Frequencies

GnomAD3 genomes AF: 0.00862 AC: 291 AN: 33762 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00186

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.000763

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00869 AC: 294 AN: 33822 Hom.: 0 Cov.: 0 AF XY: 0.00869 AC XY: 294 AN XY: 33822

African (AFR) AF: 0.0325 AC: 283 AN: 8705

American (AMR) AF: 0.00186 AC: 7 AN: 3769

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 2 AN: 768

East Asian (EAS) AF: 0.000763 AC: 1 AN: 1310

South Asian (SAS) AF: 0.00 AC: 0 AN: 1529

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3370

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.0000735 AC: 1 AN: 13604

Other (OTH) AF: 0.00 AC: 0 AN: 482

Alfa AF: 0.0393 Hom.: 319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.29

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2032639; hg19: chrY-21890177;