chr21-41754276-A-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020639.3(RIPK4):c.474+2249T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,052 control chromosomes in the GnomAD database, including 22,200 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 0.54 ( 22200 hom., cov: 33)
Consequence
RIPK4
NM_020639.3 intron
NM_020639.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Publications
1 publications found
Genes affected
RIPK4 (HGNC:496): (receptor interacting serine/threonine kinase 4) The protein encoded by this gene is a serine/threonine protein kinase that interacts with protein kinase C-delta. The encoded protein can also activate NFkappaB and is required for keratinocyte differentiation. This kinase undergoes autophosphorylation. [provided by RefSeq, Jul 2008]
RIPK4 Gene-Disease associations (from GenCC):
- Bartsocas-Papas syndrome 1Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P
- ectodermal dysplasia syndromeInheritance: AR Classification: STRONG Submitted by: Ambry Genetics
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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=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.537 AC: 81647AN: 151934Hom.: 22183 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
81647
AN:
151934
Hom.:
Cov.:
33
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: 0.537 AC: 81709AN: 152052Hom.: 22200 Cov.: 33 AF XY: 0.534 AC XY: 39677AN XY: 74318 show subpopulations
GnomAD4 genome
AF:
AC:
81709
AN:
152052
Hom.:
Cov.:
33
AF XY:
AC XY:
39677
AN XY:
74318
show subpopulations
African (AFR)
AF:
AC:
23289
AN:
41456
American (AMR)
AF:
AC:
8722
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
2093
AN:
3472
East Asian (EAS)
AF:
AC:
1715
AN:
5186
South Asian (SAS)
AF:
AC:
2630
AN:
4818
European-Finnish (FIN)
AF:
AC:
4795
AN:
10562
Middle Eastern (MID)
AF:
AC:
181
AN:
294
European-Non Finnish (NFE)
AF:
AC:
36535
AN:
67970
Other (OTH)
AF:
AC:
1149
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1990
3980
5970
7960
9950
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
714
1428
2142
2856
3570
<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:
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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