1-92902752-G-T

Variant names:

• chr1-92902752-G-T
• rs2255723
• NM_001006605.5:c.55-26322C>A

Variant summary

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

The NM_001006605.5(DIPK1A):​c.55-26322C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,066 control chromosomes in the GnomAD database, including 39,589 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 0.71 (39589 hom., cov: 31)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001006605.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK1A	NM_001006605.5	MANE Select	c.55-26322C>A		intron	N/A	NP_001006606.2	Q5T7M9-1
	DIPK1A	NM_001252269.2		c.55-51797C>A		intron	N/A	NP_001239198.1	A0A087X2C2
	DIPK1A	NM_001252270.2		c.55-26322C>A		intron	N/A	NP_001239199.1	A0A087WZK6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK1A	ENST00000370310.5	TSL:2 MANE Select	c.55-26322C>A		intron	N/A	ENSP00000359333.4	Q5T7M9-1
	DIPK1A	ENST00000615519.4	TSL:1	c.55-26322C>A		intron	N/A	ENSP00000483279.1	Q5T7M9-2
	DIPK1A	ENST00000880344.1		c.55-26322C>A		intron	N/A	ENSP00000550403.1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108471 AN: 151948 Hom.: 39539 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.714 AC: 108580 AN: 152066 Hom.: 39589 Cov.: 31 AF XY: 0.717 AC XY: 53303 AN XY: 74320

African (AFR) AF: 0.829 AC: 34391 AN: 41474

American (AMR) AF: 0.702 AC: 10728 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4933 AN: 5166

South Asian (SAS) AF: 0.825 AC: 3981 AN: 4826

European-Finnish (FIN) AF: 0.616 AC: 6498 AN: 10550

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43177 AN: 67972

Other (OTH) AF: 0.687 AC: 1452 AN: 2114

Alfa AF: 0.661 Hom.: 44148

Bravo AF: 0.724

Asia WGS AF: 0.874 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.69
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2255723; hg19: chr1-93368309;