rs931794

Variant names:

• chr15-78533838-G-A
• rs931794
• NM_001013619.4:c.*168G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-78533838-G-A
• chr15-78533838-G-C

Variant summary

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

The NM_001013619.4(HYKK):​c.*168G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 590,018 control chromosomes in the GnomAD database, including 134,807 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 0.69 (36603 hom., cov: 32)
  • Exomes 𝑓: 0.67 (98204 hom.)
• Consequence: HYKK NM_001013619.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 69 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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.*168G>A		3_prime_UTR	Exon 5 of 5	NP_001013641.2	A2RU49-1
	HYKK	NM_001083612.2		c.662-3462G>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.*168G>A		3_prime_UTR	Exon 5 of 5	ENSP00000373640.4	A2RU49-1
	HYKK	ENST00000569878.5	TSL:5	c.*168G>A		3_prime_UTR	Exon 4 of 4	ENSP00000455459.1	A2RU49-1
	HYKK	ENST00000408962.6	TSL:5	c.662-3462G>A		intron	N/A	ENSP00000386197.2	A2RU49-3

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105018 AN: 151954 Hom.: 36564 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.677

GnomAD4 exome AF: 0.668 AC: 292427 AN: 437946 Hom.: 98204 Cov.: 4 AF XY: 0.672 AC XY: 154495 AN XY: 229922

African (AFR) AF: 0.760 AC: 9297 AN: 12240

American (AMR) AF: 0.778 AC: 11863 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 8491 AN: 13482

East Asian (EAS) AF: 0.649 AC: 19687 AN: 30330

South Asian (SAS) AF: 0.742 AC: 30241 AN: 40752

European-Finnish (FIN) AF: 0.656 AC: 19314 AN: 29436

Middle Eastern (MID) AF: 0.603 AC: 1216 AN: 2018

European-Non Finnish (NFE) AF: 0.652 AC: 175382 AN: 269002

Other (OTH) AF: 0.666 AC: 16936 AN: 25430

GnomAD4 genome AF: 0.691 AC: 105111 AN: 152072 Hom.: 36603 Cov.: 32 AF XY: 0.696 AC XY: 51707 AN XY: 74336

African (AFR) AF: 0.754 AC: 31252 AN: 41474

American (AMR) AF: 0.752 AC: 11495 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3445 AN: 5166

South Asian (SAS) AF: 0.745 AC: 3590 AN: 4816

European-Finnish (FIN) AF: 0.667 AC: 7049 AN: 10572

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43960 AN: 67978

Other (OTH) AF: 0.681 AC: 1436 AN: 2110

Alfa AF: 0.665 Hom.: 52840

Bravo AF: 0.699

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.78
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs931794; hg19: chr15-78826180;