3-144037345-C-G

Position:

• chr3-144037345-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000493396.1(DIPK2A):​n.484+2665C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIPK2A	ENST00000493396.1	n.484+2665C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.370

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1025984; hg19: chr3-143756187;