rs1029233

chr21-32033387-T-Gchr21-32033387-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439107.1(HUNK):c.329-10715T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,090 control chromosomes in the GnomAD database, including 36,930 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 (36930 hom., cov: 33)
• Consequence: HUNK ENST00000439107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 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
HUNK	ENST00000439107.1	c.329-10715T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105442 AN: 151972 Hom.: 36881 Cov.: 33

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.694 AC: 105553 AN: 152090 Hom.: 36930 Cov.: 33 AF XY: 0.694 AC XY: 51588 AN XY: 74340

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.687

Alfa AF: 0.659 Hom.: 57089

Bravo AF: 0.698

Asia WGS AF: 0.561 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1029233; hg19: chr21-33405700;