21-32008727-G-A

Position:

• chr21-32008727-G-A

Variant summary

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

The ENST00000439107.1(HUNK):​c.328+12779G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,136 control chromosomes in the GnomAD database, including 3,432 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 0.19 (3432 hom., cov: 32)
• Consequence: HUNK ENST00000439107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HUNK	ENST00000439107.1	c.328+12779G>A		intron_variant		5		ENSP00000408219

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28337 AN: 152018 Hom.: 3429 Cov.: 32

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.186 AC: 28338 AN: 152136 Hom.: 3432 Cov.: 32 AF XY: 0.194 AC XY: 14414 AN XY: 74384

Gnomad4 AFR AF: 0.0414

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.214

Alfa AF: 0.220 Hom.: 6019

Bravo AF: 0.176

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2833607; hg19: chr21-33381040;