rs1559806

Positions:

• chr18-74441552-G-A
• chr18-74441552-G-C
• chr18-74441552-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001044369.3(DIPK1C):​c.1041+400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,990 control chromosomes in the GnomAD database, including 14,669 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 0.43 (14669 hom., cov: 32)
• Consequence: DIPK1C NM_001044369.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

Genes affected

DIPK1C (HGNC:31729): (divergent protein kinase domain 1C) 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. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIPK1C	NM_001044369.3	c.1041+400C>T		intron_variant		ENST00000343998.8	NP_001037834.2
DIPK1C	XM_017025551.3	c.618+400C>T		intron_variant			XP_016881040.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIPK1C	ENST00000343998.8	c.1041+400C>T		intron_variant		5	NM_001044369.3	ENSP00000344331.6
DIPK1C	ENST00000400291.2	c.144+400C>T		intron_variant		1		ENSP00000383148.2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65269 AN: 151872 Hom.: 14666 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.430 AC: 65299 AN: 151990 Hom.: 14669 Cov.: 32 AF XY: 0.437 AC XY: 32482 AN XY: 74292

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.430

Alfa AF: 0.407 Hom.: 24132

Bravo AF: 0.439

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.24

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

LitVar

Other links and lift over

dbSNP: rs1559806; hg19: chr18-72108787;