1-92883489-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.137
Variant links:
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]

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ACMG classification

Classification made for transcript

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
DIPK1ANM_001006605.5 linkc.55-7059T>C intron_variant Intron 1 of 4 ENST00000370310.5 NP_001006606.2 Q5T7M9-1
DIPK1ANM_001252269.2 linkc.55-32534T>C intron_variant Intron 1 of 3 NP_001239198.1 A0A087X2C2
DIPK1ANM_001252270.2 linkc.55-7059T>C intron_variant Intron 1 of 3 NP_001239199.1 A0A087WZK6
DIPK1ANM_001252273.2 linkc.55-7059T>C intron_variant Intron 1 of 4 NP_001239202.1 Q5T7M9-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DIPK1AENST00000370310.5 linkc.55-7059T>C intron_variant Intron 1 of 4 2 NM_001006605.5 ENSP00000359333.4 Q5T7M9-1
DIPK1AENST00000615519.4 linkc.55-7059T>C intron_variant Intron 1 of 4 1 ENSP00000483279.1 Q5T7M9-2
DIPK1AENST00000613902.4 linkc.55-32534T>C intron_variant Intron 1 of 3 4 ENSP00000484866.1 A0A087X2C2
DIPK1AENST00000616709.4 linkc.55-7059T>C intron_variant Intron 1 of 3 3 ENSP00000482718.1 A0A087WZK6

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7536563; hg19: chr1-93349046; API