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GeneBe

rs8034191

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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 152038 control chromosomes in the gnomAD Genomes database, including 6409 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 0.27 ( 6409 hom., cov: 32)

Consequence

HYKK
NM_001013619.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.649

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd 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
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
6.8
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