rs11164838

Variant names:

• chr1-92929821-C-T
• rs11164838
• NM_001006605.5:c.54+31555G>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.54+31555G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,962 control chromosomes in the GnomAD database, including 12,007 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 0.37 (12007 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 6 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]

ENSG00000296280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.54+31555G>A		intron_variant	Intron 1 of 4	ENST00000370310.5	NP_001006606.2
DIPK1A	NM_001252269.2	c.54+31555G>A		intron_variant	Intron 1 of 3		NP_001239198.1
DIPK1A	NM_001252270.2	c.54+31555G>A		intron_variant	Intron 1 of 3		NP_001239199.1
DIPK1A	NM_001252273.2	c.54+31555G>A		intron_variant	Intron 1 of 4		NP_001239202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIPK1A	ENST00000370310.5	c.54+31555G>A		intron_variant	Intron 1 of 4	2	NM_001006605.5	ENSP00000359333.4

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55515 AN: 151844 Hom.: 12003 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.365 AC: 55528 AN: 151962 Hom.: 12007 Cov.: 32 AF XY: 0.368 AC XY: 27329 AN XY: 74258

African (AFR) AF: 0.139 AC: 5761 AN: 41462

American (AMR) AF: 0.407 AC: 6210 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1824 AN: 3472

East Asian (EAS) AF: 0.722 AC: 3738 AN: 5176

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4814

European-Finnish (FIN) AF: 0.424 AC: 4457 AN: 10522

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29892 AN: 67944

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.402 Hom.: 9376

Bravo AF: 0.356

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.65
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs11164838; hg19: chr1-93395378;