1-92883489-A-G

Variant names:

• chr1-92883489-A-G
• rs7536563
• NM_001006605.5:c.55-7059T>C

Variant summary

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

The NM_001006605.5(DIPK1A):​c.55-7059T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,008 control chromosomes in the GnomAD database, including 27,591 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 0.59 (27591 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

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 rank	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.55-7059T>C		intron_variant	Intron 1 of 4	ENST00000370310.5	NP_001006606.2
DIPK1A	NM_001252269.2	c.55-32534T>C		intron_variant	Intron 1 of 3		NP_001239198.1
DIPK1A	NM_001252270.2	c.55-7059T>C		intron_variant	Intron 1 of 3		NP_001239199.1
DIPK1A	NM_001252273.2	c.55-7059T>C		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.55-7059T>C		intron_variant	Intron 1 of 4	2	NM_001006605.5	ENSP00000359333.4
DIPK1A	ENST00000615519.4	c.55-7059T>C		intron_variant	Intron 1 of 4	1		ENSP00000483279.1
DIPK1A	ENST00000613902.4	c.55-32534T>C		intron_variant	Intron 1 of 3	4		ENSP00000484866.1
DIPK1A	ENST00000616709.4	c.55-7059T>C		intron_variant	Intron 1 of 3	3		ENSP00000482718.1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89389 AN: 151890 Hom.: 27589 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.588 AC: 89408 AN: 152008 Hom.: 27591 Cov.: 32 AF XY: 0.593 AC XY: 44091 AN XY: 74300

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.581

Alfa AF: 0.617 Hom.: 28535

Bravo AF: 0.582

Asia WGS AF: 0.780 AC: 2710 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	3.3
DANN	Benign	0.73

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: rs7536563; hg19: chr1-93349046;