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. 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HUNK	ENST00000439107.1	c.328+16925A>G		intron_variant	Intron 4 of 4	5		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

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;