chrY-19727881-A-G

Variant names:

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

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>C 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 0.56 (0 hom., 17729 hem., cov: 0)
  • Failed GnomAD Quality Control
• 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=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KDM5D	NM_004653.5	c.1371+3891T>C		intron_variant	Intron 11 of 26	ENST00000317961.9	NP_004644.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KDM5D	ENST00000317961.9	c.1371+3891T>C		intron_variant	Intron 11 of 26	1	NM_004653.5	ENSP00000322408.4

Frequencies

GnomAD3 genomes AF: 0.562 AC: 17673 AN: 31419 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.955

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.542

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.563 AC: 17729 AN: 31478 Hom.: 0 Cov.: 0 AF XY: 0.563 AC XY: 17729 AN XY: 31478

African (AFR) AF: 0.788 AC: 6275 AN: 7968

American (AMR) AF: 0.375 AC: 1301 AN: 3466

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 573 AN: 740

East Asian (EAS) AF: 0.984 AC: 1184 AN: 1203

South Asian (SAS) AF: 0.506 AC: 718 AN: 1419

European-Finnish (FIN) AF: 0.933 AC: 2689 AN: 2883

Middle Eastern (MID) AF: 0.954 AC: 62 AN: 65

European-Non Finnish (NFE) AF: 0.354 AC: 4630 AN: 13084

Other (OTH) AF: 0.550 AC: 243 AN: 442

Alfa AF: 0.230 Hom.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

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;