GeneBe

rs71268283

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_003821.6(RIPK2):​c.1029+10_1029+25delAAAAAAAAAAAAAAAA variant causes a intron change. The variant allele was found at a frequency of 0.0000752 in 558,334 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00027 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000035 ( 0 hom. )

Consequence

RIPK2
NM_003821.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.92

Publications

0 publications found
Variant links:
Genes affected
RIPK2 (HGNC:10020): (receptor interacting serine/threonine kinase 2) This gene encodes a member of the receptor-interacting protein (RIP) family of serine/threonine protein kinases. The encoded protein contains a C-terminal caspase activation and recruitment domain (CARD), and is a component of signaling complexes in both the innate and adaptive immune pathways. It is a potent activator of NF-kappaB and inducer of apoptosis in response to various stimuli. [provided by RefSeq, Jul 2008]
PARAIL (HGNC:55545): (palmitic acid regulated anti-inflammatory lncRNA)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High AC in GnomAd4 at 26 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RIPK2NM_003821.6 linkc.1029+10_1029+25delAAAAAAAAAAAAAAAA intron_variant Intron 8 of 10 ENST00000220751.5 NP_003812.1 O43353-1A0A0S2Z4Z8
RIPK2NM_001375360.1 linkc.618+10_618+25delAAAAAAAAAAAAAAAA intron_variant Intron 7 of 9 NP_001362289.1
RIPK2XM_011517357.3 linkc.516+10_516+25delAAAAAAAAAAAAAAAA intron_variant Intron 6 of 8 XP_011515659.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RIPK2ENST00000220751.5 linkc.1029+10_1029+25delAAAAAAAAAAAAAAAA intron_variant Intron 8 of 10 1 NM_003821.6 ENSP00000220751.4 O43353-1

Frequencies

GnomAD3 genomes
AF:
0.000268
AC:
26
AN:
97062
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00111
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000347
AC:
16
AN:
461264
Hom.:
0
AF XY:
0.0000292
AC XY:
7
AN XY:
240056
show subpopulations
African (AFR)
AF:
0.00137
AC:
13
AN:
9520
American (AMR)
AF:
0.00
AC:
0
AN:
11044
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10276
East Asian (EAS)
AF:
0.00
AC:
0
AN:
20676
South Asian (SAS)
AF:
0.00
AC:
0
AN:
25888
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28494
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1686
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
331326
Other (OTH)
AF:
0.000134
AC:
3
AN:
22354
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.638
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000268
AC:
26
AN:
97070
Hom.:
0
Cov.:
0
AF XY:
0.000249
AC XY:
11
AN XY:
44206
show subpopulations
African (AFR)
AF:
0.00111
AC:
26
AN:
23468
American (AMR)
AF:
0.00
AC:
0
AN:
8918
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2796
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2856
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2446
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2610
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
206
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
51758
Other (OTH)
AF:
0.00
AC:
0
AN:
1292
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.696
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs71268283; hg19: chr8-90796369; API