21-32012873-A-G

Position:

• chr21-32012873-A-G

Variant summary

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

The ENST00000439107.1(HUNK):​c.328+16925A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,906 control chromosomes in the GnomAD database, including 27,503 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 0.60 (27503 hom., cov: 31)
• Consequence: HUNK ENST00000439107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

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 = 0.643 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.328+16925A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90419 AN: 151788 Hom.: 27468 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.596 AC: 90511 AN: 151906 Hom.: 27503 Cov.: 31 AF XY: 0.591 AC XY: 43856 AN XY: 74244

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.540

Alfa AF: 0.595 Hom.: 42133

Bravo AF: 0.584

Asia WGS AF: 0.502 AC: 1746 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	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2833610; hg19: chr21-33385186;