rs12745968

chr1-92936280-A-G

Variant summary

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

The NM_001006605.5(DIPK1A):c.54+25096T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,070 control chromosomes in the GnomAD database, including 9,747 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 0.35 (9747 hom., cov: 31)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

DIPK1A (HGNC:32213): (divergent protein kinase domain 1A) This gene encodes a member of the FAM69 family of cysteine-rich type II transmembrane proteins. These proteins localize to the endoplasmic reticulum but their specific functions are unknown. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIPK1A	NM_001006605.5	c.54+25096T>C		intron_variant		ENST00000370310.5
DIPK1A	NM_001252269.2	c.54+25096T>C		intron_variant
DIPK1A	NM_001252270.2	c.54+25096T>C		intron_variant
DIPK1A	NM_001252273.2	c.54+25096T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIPK1A	ENST00000370310.5	c.54+25096T>C		intron_variant		2	NM_001006605.5	P1
DIPK1A	ENST00000615519.4	c.54+25096T>C		intron_variant		1
DIPK1A	ENST00000613902.4	c.54+25096T>C		intron_variant		4
DIPK1A	ENST00000616709.4	c.54+25096T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53119 AN: 151952 Hom.: 9736 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.350 AC: 53172 AN: 152070 Hom.: 9747 Cov.: 31 AF XY: 0.345 AC XY: 25666 AN XY: 74334

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.362

Alfa AF: 0.349 Hom.: 12023

Bravo AF: 0.347

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12745968; hg19: chr1-93401837;