15-78510244-G-A

Variant names:

• chr15-78510244-G-A
• rs9788682
• NM_001013619.4:c.-6+2573G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001013619.4(HYKK):​c.-6+2573G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,152 control chromosomes in the GnomAD database, including 4,316 homozygotes. 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 0.22 (4316 hom., cov: 29)
• Consequence: HYKK NM_001013619.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606
• Publications: 19 publications found

Genes affected

HYKK (HGNC:34403): (hydroxylysine kinase) Enables hydroxylysine kinase activity. Predicted to be involved in lysine catabolic process. Predicted to be located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

HYKK Gene-Disease associations (from GenCC):

• inborn disorder of lysine and hydroxylysine metabolism

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013619.4. 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
	HYKK	NM_001013619.4	MANE Select	c.-6+2573G>A		intron	N/A	NP_001013641.2	A2RU49-1
	HYKK	NM_001083612.2		c.-6+2573G>A		intron	N/A	NP_001077081.1	A2RU49-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYKK	ENST00000388988.9	TSL:5 MANE Select	c.-6+2573G>A		intron	N/A	ENSP00000373640.4	A2RU49-1
	HYKK	ENST00000566332.5	TSL:1	c.-6+2573G>A		intron	N/A	ENSP00000457154.1	A0A0C4DGM4
	HYKK	ENST00000408962.6	TSL:5	c.-6+2573G>A		intron	N/A	ENSP00000386197.2	A2RU49-3

Frequencies

GnomAD3 genomes AF: 0.225 AC: 33947 AN: 151038 Hom.: 4309 Cov.: 29

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.225 AC: 33968 AN: 151152 Hom.: 4316 Cov.: 29 AF XY: 0.232 AC XY: 17124 AN XY: 73806

African (AFR) AF: 0.163 AC: 6696 AN: 41124

American (AMR) AF: 0.405 AC: 6156 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 657 AN: 3462

East Asian (EAS) AF: 0.277 AC: 1420 AN: 5128

South Asian (SAS) AF: 0.366 AC: 1751 AN: 4778

European-Finnish (FIN) AF: 0.241 AC: 2491 AN: 10340

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14092 AN: 67822

Other (OTH) AF: 0.234 AC: 487 AN: 2084

Alfa AF: 0.133 Hom.: 292

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

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: rs9788682; hg19: chr15-78802586;