chr1-92858414-T-C

Position:

• chr1-92858414-T-C

Variant summary

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

The NM_001006605.5(DIPK1A):​c.190-7459A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,042 control chromosomes in the GnomAD database, including 29,296 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 0.61 (29296 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.190-7459A>G		intron_variant		ENST00000370310.5	NP_001006606.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIPK1A	ENST00000370310.5	c.190-7459A>G		intron_variant		2	NM_001006605.5	ENSP00000359333.4

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92238 AN: 151924 Hom.: 29293 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.607 AC: 92256 AN: 152042 Hom.: 29296 Cov.: 32 AF XY: 0.611 AC XY: 45418 AN XY: 74294

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.596

Alfa AF: 0.662 Hom.: 42018

Bravo AF: 0.602

Asia WGS AF: 0.782 AC: 2719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.56

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: rs10874746; hg19: chr1-93323971;