rs8129832

Variant summary

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

The ENST00000439107.1(HUNK):​c.329-9026G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0267 in 152,236 control chromosomes in the GnomAD database, including 155 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 0.027 ( 155 hom., cov: 32)

Consequence

HUNK
ENST00000439107.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.362
Variant links:
Genes affected
HUNK (HGNC:13326): (hormonally up-regulated Neu-associated kinase) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in intracellular signal transduction and protein phosphorylation. [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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HUNKENST00000439107.1 linkuse as main transcriptc.329-9026G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0267
AC:
4059
AN:
152118
Hom.:
156
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0895
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0117
Gnomad ASJ
AF:
0.0173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000882
Gnomad OTH
AF:
0.0249
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0267
AC:
4062
AN:
152236
Hom.:
155
Cov.:
32
AF XY:
0.0259
AC XY:
1926
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0893
Gnomad4 AMR
AF:
0.0117
Gnomad4 ASJ
AF:
0.0173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000416
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000882
Gnomad4 OTH
AF:
0.0246
Alfa
AF:
0.0223
Hom.:
14
Bravo
AF:
0.0304
Asia WGS
AF:
0.00202
AC:
7
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.0
DANN
Benign
0.78

Splicing

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: rs8129832; hg19: chr21-33407389; API