rs2833607

Variant names:

• chr21-32008727-G-A
• rs2833607
• ENST00000439107.1:c.328+12779G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439107.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HUNK	ENST00000439107.1	TSL:5	c.328+12779G>A		intron	N/A	ENSP00000408219.1

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

African (AFR) AF: 0.0414 AC: 1719 AN: 41542

American (AMR) AF: 0.265 AC: 4049 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1420 AN: 5172

South Asian (SAS) AF: 0.288 AC: 1386 AN: 4820

European-Finnish (FIN) AF: 0.280 AC: 2959 AN: 10578

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15024 AN: 67962

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.209 Hom.: 8968

Bravo AF: 0.176

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.44
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2833607; hg19: chr21-33381040;