chr1-92855312-C-T

Variant names:

• chr1-92855312-C-T
• rs7514280
• NM_001006605.5:c.190-4357G>A

Variant summary

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

The NM_001006605.5(DIPK1A):​c.190-4357G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,820 control chromosomes in the GnomAD database, including 4,386 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 0.23 (4386 hom., cov: 31)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.190-4357G>A		intron_variant	Intron 2 of 4	ENST00000370310.5	NP_001006606.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIPK1A	ENST00000370310.5	c.190-4357G>A		intron_variant	Intron 2 of 4	2	NM_001006605.5	ENSP00000359333.4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35119 AN: 151702 Hom.: 4382 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.231 AC: 35137 AN: 151820 Hom.: 4386 Cov.: 31 AF XY: 0.229 AC XY: 17015 AN XY: 74172

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0151

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.246

Alfa AF: 0.157 Hom.: 359

Bravo AF: 0.226

Asia WGS AF: 0.0980 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.58

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: rs7514280; hg19: chr1-93320869;