chr1-92955350-G-A

Variant names:

• chr1-92955350-G-A
• rs4847386
• NM_001006605.5:c.54+6026C>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.54+6026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,984 control chromosomes in the GnomAD database, including 15,882 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 0.45 (15882 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.54+6026C>T		intron_variant	Intron 1 of 4	ENST00000370310.5	NP_001006606.2
DIPK1A	NM_001252269.2	c.54+6026C>T		intron_variant	Intron 1 of 3		NP_001239198.1
DIPK1A	NM_001252270.2	c.54+6026C>T		intron_variant	Intron 1 of 3		NP_001239199.1
DIPK1A	NM_001252273.2	c.54+6026C>T		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.54+6026C>T		intron_variant	Intron 1 of 4	2	NM_001006605.5	ENSP00000359333.4
DIPK1A	ENST00000615519.4	c.54+6026C>T		intron_variant	Intron 1 of 4	1		ENSP00000483279.1
DIPK1A	ENST00000613902.4	c.54+6026C>T		intron_variant	Intron 1 of 3	4		ENSP00000484866.1
DIPK1A	ENST00000616709.4	c.54+6026C>T		intron_variant	Intron 1 of 3	3		ENSP00000482718.1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68577 AN: 151866 Hom.: 15878 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.451 AC: 68606 AN: 151984 Hom.: 15882 Cov.: 32 AF XY: 0.453 AC XY: 33638 AN XY: 74298

African (AFR) AF: 0.386 AC: 16006 AN: 41472

American (AMR) AF: 0.445 AC: 6794 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3689 AN: 5174

South Asian (SAS) AF: 0.519 AC: 2504 AN: 4824

European-Finnish (FIN) AF: 0.449 AC: 4734 AN: 10532

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31615 AN: 67942

Other (OTH) AF: 0.428 AC: 903 AN: 2108

Alfa AF: 0.466 Hom.: 8851

Bravo AF: 0.448

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.22
PhyloP100		-0.13
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: rs4847386; hg19: chr1-93420907;