rs11164835

Variant names:

• chr1-92913536-G-A
• rs11164835
• NM_001006605.5:c.55-37106C>T

Variant summary

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

The NM_001006605.5(DIPK1A):​c.55-37106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,116 control chromosomes in the GnomAD database, including 9,612 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 0.35 (9612 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.369 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK1A	NM_001006605.5	MANE Select	c.55-37106C>T		intron	N/A	NP_001006606.2
	DIPK1A	NM_001252269.2		c.54+47840C>T		intron	N/A	NP_001239198.1
	DIPK1A	NM_001252270.2		c.55-37106C>T		intron	N/A	NP_001239199.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK1A	ENST00000370310.5	TSL:2 MANE Select	c.55-37106C>T		intron	N/A	ENSP00000359333.4
	DIPK1A	ENST00000615519.4	TSL:1	c.55-37106C>T		intron	N/A	ENSP00000483279.1
	DIPK1A	ENST00000613902.4	TSL:4	c.54+47840C>T		intron	N/A	ENSP00000484866.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52709 AN: 151998 Hom.: 9601 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.347 AC: 52758 AN: 152116 Hom.: 9612 Cov.: 32 AF XY: 0.342 AC XY: 25461 AN XY: 74348

African (AFR) AF: 0.374 AC: 15532 AN: 41492

American (AMR) AF: 0.325 AC: 4964 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3472

East Asian (EAS) AF: 0.0530 AC: 275 AN: 5188

South Asian (SAS) AF: 0.194 AC: 935 AN: 4826

European-Finnish (FIN) AF: 0.385 AC: 4078 AN: 10584

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24946 AN: 67968

Other (OTH) AF: 0.362 AC: 763 AN: 2110

Alfa AF: 0.332 Hom.: 2945

Bravo AF: 0.344

Asia WGS AF: 0.182 AC: 636 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	0.57
DANN	Benign	0.44
PhyloP100		-0.14
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: rs11164835; hg19: chr1-93379093;