21-32033387-T-G

Variant names:

• chr21-32033387-T-G
• rs1029233
• ENST00000439107.1:c.329-10715T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HUNK	ENST00000439107.1	c.329-10715T>G		intron_variant	Intron 4 of 4	5		ENSP00000408219.1

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

African (AFR) AF: 0.784 AC: 32539 AN: 41496

American (AMR) AF: 0.703 AC: 10743 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2811 AN: 5154

South Asian (SAS) AF: 0.564 AC: 2714 AN: 4816

European-Finnish (FIN) AF: 0.690 AC: 7304 AN: 10582

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45095 AN: 67966

Other (OTH) AF: 0.687 AC: 1454 AN: 2116

Alfa AF: 0.668 Hom.: 131960

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1029233; hg19: chr21-33405700;