chr1-92955350-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_001006605.5 intron
Scores
2
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]
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ACMG classification
Classification was made for transcript
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: 68577AN: 151866Hom.: 15878 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
68577
AN:
151866
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.451 AC: 68606AN: 151984Hom.: 15882 Cov.: 32 AF XY: 0.453 AC XY: 33638AN XY: 74298 show subpopulations
GnomAD4 genome
AF:
AC:
68606
AN:
151984
Hom.:
Cov.:
32
AF XY:
AC XY:
33638
AN XY:
74298
show subpopulations
African (AFR)
AF:
AC:
16006
AN:
41472
American (AMR)
AF:
AC:
6794
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
1950
AN:
3468
East Asian (EAS)
AF:
AC:
3689
AN:
5174
South Asian (SAS)
AF:
AC:
2504
AN:
4824
European-Finnish (FIN)
AF:
AC:
4734
AN:
10532
Middle Eastern (MID)
AF:
AC:
133
AN:
294
European-Non Finnish (NFE)
AF:
AC:
31615
AN:
67942
Other (OTH)
AF:
AC:
903
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1940
3879
5819
7758
9698
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
636
1272
1908
2544
3180
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1928
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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