chrY-19703935-G-A

Variant names:

• chrY-19703935-G-A
• rs2032629
• NM_004653.5:c.*2060C>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.*2060C>T variant causes a 3 prime UTR 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 0.0047 (0 hom., 157 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: KDM5D NM_004653.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 4 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=-0.87).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00467 (157/33654) while in subpopulation AMR AF = 0.0208 (78/3749). AF 95% confidence interval is 0.0171. There are 0 homozygotes in GnomAd4. There are 157 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 157 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM5D	NM_004653.5	MANE Select	c.*2060C>T		3_prime_UTR	Exon 27 of 27	NP_004644.2
	KDM5D	NM_001146705.2		c.*2060C>T		3_prime_UTR	Exon 28 of 28	NP_001140177.1
	KDM5D	NM_001146706.2		c.*2060C>T		3_prime_UTR	Exon 26 of 26	NP_001140178.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM5D	ENST00000317961.9	TSL:1 MANE Select	c.*2060C>T		3_prime_UTR	Exon 27 of 27	ENSP00000322408.4
	KDM5D	ENST00000469599.6	TSL:2	n.5431C>T		non_coding_transcript_exon	Exon 12 of 12

Frequencies

GnomAD3 genomes AF: 0.00467 AC: 157 AN: 33592 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00151

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.00390

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00420

Gnomad OTH AF: 0.0127

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.00467 AC: 157 AN: 33654 Hom.: 0 Cov.: 0 AF XY: 0.00467 AC XY: 157 AN XY: 33654

African (AFR) AF: 0.00150 AC: 13 AN: 8674

American (AMR) AF: 0.0208 AC: 78 AN: 3749

Ashkenazi Jewish (ASJ) AF: 0.00390 AC: 3 AN: 770

East Asian (EAS) AF: 0.00 AC: 0 AN: 1299

South Asian (SAS) AF: 0.00 AC: 0 AN: 1512

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3313

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

European-Non Finnish (NFE) AF: 0.00420 AC: 57 AN: 13574

Other (OTH) AF: 0.0126 AC: 6 AN: 477

Alfa AF: 0.0255 Hom.: 1096

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2032629; hg19: chrY-21865821;