chr3-144017429-A-C

Position:

• chr3-144017429-A-C

Variant summary

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

The ENST00000493396.1(DIPK2A):​n.354-17121A>C 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 0.0796 in 152,154 control chromosomes in the GnomAD database, including 1,351 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 0.080 (1351 hom., cov: 32)
• Consequence: DIPK2A ENST00000493396.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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.354-17121A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12085 AN: 152036 Hom.: 1348 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00982

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0796 AC: 12104 AN: 152154 Hom.: 1351 Cov.: 32 AF XY: 0.0759 AC XY: 5644 AN XY: 74392

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.0297

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00983

Gnomad4 OTH AF: 0.0606

Alfa AF: 0.0179 Hom.: 69

Bravo AF: 0.0886

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513238; hg19: chr3-143736271;