rs2833610

Variant names:

• chr21-32012873-A-G
• rs2833610
• ENST00000439107.1:c.328+16925A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-32012873-A-G
• chr21-32012873-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 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 = 0.643 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+16925A>G		intron	N/A	ENSP00000408219.1

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

African (AFR) AF: 0.650 AC: 26892 AN: 41372

American (AMR) AF: 0.444 AC: 6785 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3468

East Asian (EAS) AF: 0.441 AC: 2271 AN: 5148

South Asian (SAS) AF: 0.507 AC: 2441 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6722 AN: 10568

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42036 AN: 67952

Other (OTH) AF: 0.540 AC: 1138 AN: 2108

Alfa AF: 0.596 Hom.: 69644

Bravo AF: 0.584

Asia WGS AF: 0.502 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2833610; hg19: chr21-33385186;