1-92868581-C-T

Variant names:

• chr1-92868581-C-T
• rs2811600
• NM_001006605.5:c.189+7715G>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.189+7715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,072 control chromosomes in the GnomAD database, including 36,260 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 0.69 (36260 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.189+7715G>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.189+7715G>A		intron_variant	Intron 2 of 4	2	NM_001006605.5	ENSP00000359333.4

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104182 AN: 151954 Hom.: 36214 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.686 AC: 104281 AN: 152072 Hom.: 36260 Cov.: 32 AF XY: 0.690 AC XY: 51259 AN XY: 74318

African (AFR) AF: 0.731 AC: 30295 AN: 41462

American (AMR) AF: 0.690 AC: 10540 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2641 AN: 3466

East Asian (EAS) AF: 0.955 AC: 4947 AN: 5182

South Asian (SAS) AF: 0.825 AC: 3976 AN: 4820

European-Finnish (FIN) AF: 0.616 AC: 6508 AN: 10560

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43181 AN: 67976

Other (OTH) AF: 0.671 AC: 1418 AN: 2114

Alfa AF: 0.687 Hom.: 12288

Bravo AF: 0.692

Asia WGS AF: 0.870 AC: 3024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		0.45
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

Publications

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Other links and lift over

dbSNP: rs2811600; hg19: chr1-93334138;