rs11164838

Positions:

• chr1-92929821-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.81).
• 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/exons	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.54+31555G>A		intron_variant		ENST00000370310.5	NP_001006606.2
DIPK1A	NM_001252269.2	c.54+31555G>A		intron_variant			NP_001239198.1
DIPK1A	NM_001252270.2	c.54+31555G>A		intron_variant			NP_001239199.1
DIPK1A	NM_001252273.2	c.54+31555G>A		intron_variant			NP_001239202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIPK1A	ENST00000370310.5	c.54+31555G>A		intron_variant		2	NM_001006605.5	ENSP00000359333.4
DIPK1A	ENST00000615519.4	c.54+31555G>A		intron_variant		1		ENSP00000483279.1
DIPK1A	ENST00000613902.4	c.54+31555G>A		intron_variant		4		ENSP00000484866.1
DIPK1A	ENST00000616709.4	c.54+31555G>A		intron_variant		3		ENSP00000482718.1

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.366

Alfa AF: 0.408 Hom.: 6628

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11164838; hg19: chr1-93395378;