3-144037345-C-G

Variant names:

• chr3-144037345-C-G
• rs1025984
• ENST00000493396.1:n.484+2665C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000493396.1(DIPK2A):​n.484+2665C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,978 control chromosomes in the GnomAD database, including 12,040 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 0.38 (12040 hom., cov: 33)
• Consequence: DIPK2A ENST00000493396.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 1 publications found

Genes affected

DIPK2A (HGNC:28490): (divergent protein kinase domain 2A) Involved in several processes, including cardiac muscle cell proliferation; negative regulation of smooth muscle cell apoptotic process; and positive regulation of protein kinase C activity. Located in Golgi membrane and extracellular space. Part of COPI vesicle coat. [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=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 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
DIPK2A	ENST00000493396.1	n.484+2665C>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58226 AN: 151862 Hom.: 12014 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.383 AC: 58278 AN: 151978 Hom.: 12040 Cov.: 33 AF XY: 0.379 AC XY: 28188 AN XY: 74282

African (AFR) AF: 0.542 AC: 22457 AN: 41458

American (AMR) AF: 0.296 AC: 4519 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1108 AN: 5180

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4822

European-Finnish (FIN) AF: 0.341 AC: 3585 AN: 10518

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23166 AN: 67966

Other (OTH) AF: 0.370 AC: 778 AN: 2102

Alfa AF: 0.233 Hom.: 536

Bravo AF: 0.384

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.32
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1025984; hg19: chr3-143756187;