rs2032623

Variant names:

• chrY-19716186-G-GT
• rs2032623
• NM_004653.5:c.2031+92_2031+93insA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_004653.5(KDM5D):​c.2031+92_2031+93insA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0058 (0 hom., 200 hem., cov: 0)
  • Exomes 𝑓: 0.00065 (0 hom. 149 hem.)
• Consequence: KDM5D NM_004653.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00583 (200/34293) while in subpopulation AFR AF= 0.0217 (191/8814). AF 95% confidence interval is 0.0192. There are 0 homozygotes in gnomad4. There are 200 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Hemizygotes in GnomAd4 at 200 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KDM5D	NM_004653.5	c.2031+92_2031+93insA		intron_variant	Intron 15 of 26	ENST00000317961.9	NP_004644.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KDM5D	ENST00000317961.9	c.2031+92_2031+93insA		intron_variant	Intron 15 of 26	1	NM_004653.5	ENSP00000322408.4

Frequencies

GnomAD3 genomes AF: 0.00549 AC: 188 AN: 34231 Hom.: 0 Cov.: 0 AF XY: 0.00549 AC XY: 188 AN XY: 34231

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000646

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00210

GnomAD4 exome AF: 0.000655 AC: 149 AN: 227644 Hom.: 0 Cov.: 0 AF XY: 0.000655 AC XY: 149 AN XY: 227644

Gnomad4 AFR exome AF: 0.0243

Gnomad4 AMR exome AF: 0.000999

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000721

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000338

Gnomad4 OTH exome AF: 0.00151

GnomAD4 genome AF: 0.00583 AC: 200 AN: 34293 Hom.: 0 Cov.: 0 AF XY: 0.00583 AC XY: 200 AN XY: 34293

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.00182

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000644

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00208

Alfa AF: 0.000357 Hom.: 5

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032623; hg19: chrY-21878072;