rs2833607

Variant names:

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HUNK	ENST00000439107.1	c.328+12779G>A		intron_variant	Intron 4 of 4	5		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

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;