1-92858414-T-C

Variant names:

• chr1-92858414-T-C
• rs10874746
• NM_001006605.5:c.190-7459A>G

Variant summary

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

The NM_001006605.5(DIPK1A):​c.190-7459A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,042 control chromosomes in the GnomAD database, including 29,296 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 0.61 (29296 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 46 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 = 0.922 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.190-7459A>G		intron	N/A	NP_001006606.2	Q5T7M9-1
	DIPK1A	NM_001252271.2		c.115-7459A>G		intron	N/A	NP_001239200.1	A0A087WZ97
	DIPK1A	NM_001252269.2		c.55-7459A>G		intron	N/A	NP_001239198.1	A0A087X2C2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK1A	ENST00000370310.5	TSL:2 MANE Select	c.190-7459A>G		intron	N/A	ENSP00000359333.4	Q5T7M9-1
	DIPK1A	ENST00000615519.4	TSL:1	c.190-7459A>G		intron	N/A	ENSP00000483279.1	Q5T7M9-2
	DIPK1A	ENST00000613047.4	TSL:4	c.115-7459A>G		intron	N/A	ENSP00000482478.1	A0A087WZ97

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92238 AN: 151924 Hom.: 29293 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.607 AC: 92256 AN: 152042 Hom.: 29296 Cov.: 32 AF XY: 0.611 AC XY: 45418 AN XY: 74294

African (AFR) AF: 0.432 AC: 17885 AN: 41442

American (AMR) AF: 0.655 AC: 10002 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2602 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4885 AN: 5172

South Asian (SAS) AF: 0.774 AC: 3728 AN: 4814

European-Finnish (FIN) AF: 0.628 AC: 6642 AN: 10570

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44437 AN: 67984

Other (OTH) AF: 0.596 AC: 1257 AN: 2110

Alfa AF: 0.649 Hom.: 96172

Bravo AF: 0.602

Asia WGS AF: 0.782 AC: 2719 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	0.11
DANN	Benign	0.56
PhyloP100		-2.2
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: rs10874746; hg19: chr1-93323971;