rs8034191

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1

The NM_001013619.4(HYKK):​c.337+256T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,156 control chromosomes in the GnomAD database, including 6,412 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).

Frequency

Genomes: 𝑓 0.27 ( 6412 hom., cov: 32)

Consequence

HYKK
NM_001013619.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.649
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PP5
Variant 15-78513681-T-C is Pathogenic according to our data. Variant chr15-78513681-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3336640.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89). . Strength limited to SUPPORTING due to the PP5.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HYKKNM_001013619.4 linkuse as main transcriptc.337+256T>C intron_variant ENST00000388988.9
HYKKNM_001083612.2 linkuse as main transcriptc.337+256T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HYKKENST00000388988.9 linkuse as main transcriptc.337+256T>C intron_variant 5 NM_001013619.4 P1A2RU49-1

Frequencies

GnomAD3 genomes
AF:
0.272
AC:
41387
AN:
152038
Hom.:
6409
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.407
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.345
Gnomad EAS
AF:
0.0286
Gnomad SAS
AF:
0.234
Gnomad FIN
AF:
0.332
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.351
Gnomad OTH
AF:
0.290
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.272
AC:
41417
AN:
152156
Hom.:
6412
Cov.:
32
AF XY:
0.269
AC XY:
19987
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.232
Gnomad4 ASJ
AF:
0.345
Gnomad4 EAS
AF:
0.0289
Gnomad4 SAS
AF:
0.235
Gnomad4 FIN
AF:
0.332
Gnomad4 NFE
AF:
0.351
Gnomad4 OTH
AF:
0.287
Alfa
AF:
0.328
Hom.:
19811
Bravo
AF:
0.260
Asia WGS
AF:
0.138
AC:
482
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.9
DANN
Benign
0.35

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8034191; hg19: chr15-78806023; COSMIC: COSV64762226; API