8-89772777-C-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_003821.6(RIPK2):​c.802C>G​(p.Leu268Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,610,338 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.0074 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00070 ( 16 hom. )

Consequence

RIPK2
NM_003821.6 missense

Scores

8
10

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.75
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.013203502).
BP6
Variant 8-89772777-C-G is Benign according to our data. Variant chr8-89772777-C-G is described in ClinVar as [Benign]. Clinvar id is 791293.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00736 (1119/152086) while in subpopulation AFR AF = 0.0255 (1059/41492). AF 95% confidence interval is 0.0242. There are 12 homozygotes in GnomAd4. There are 508 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
BS2
High AC in GnomAd4 at 1119 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RIPK2NM_003821.6 linkc.802C>G p.Leu268Val missense_variant Exon 6 of 11 ENST00000220751.5 NP_003812.1 O43353-1A0A0S2Z4Z8
RIPK2NM_001375360.1 linkc.391C>G p.Leu131Val missense_variant Exon 5 of 10 NP_001362289.1
RIPK2XM_011517357.3 linkc.289C>G p.Leu97Val missense_variant Exon 4 of 9 XP_011515659.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RIPK2ENST00000220751.5 linkc.802C>G p.Leu268Val missense_variant Exon 6 of 11 1 NM_003821.6 ENSP00000220751.4 O43353-1
RIPK2ENST00000522965.1 linkn.*441C>G non_coding_transcript_exon_variant Exon 5 of 10 1 ENSP00000429271.1 E7ERW9
RIPK2ENST00000522965.1 linkn.*441C>G 3_prime_UTR_variant Exon 5 of 10 1 ENSP00000429271.1 E7ERW9

Frequencies

GnomAD3 genomes
AF:
0.00736
AC:
1118
AN:
151968
Hom.:
12
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0256
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00210
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00719
GnomAD2 exomes
AF:
0.00183
AC:
456
AN:
248534
AF XY:
0.00133
show subpopulations
Gnomad AFR exome
AF:
0.0256
Gnomad AMR exome
AF:
0.00103
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000178
Gnomad OTH exome
AF:
0.000663
GnomAD4 exome
AF:
0.000704
AC:
1027
AN:
1458252
Hom.:
16
Cov.:
29
AF XY:
0.000608
AC XY:
441
AN XY:
725364
show subpopulations
Gnomad4 AFR exome
AF:
0.0265
AC:
882
AN:
33262
Gnomad4 AMR exome
AF:
0.00102
AC:
45
AN:
44210
Gnomad4 ASJ exome
AF:
0.00
AC:
0
AN:
26006
Gnomad4 EAS exome
AF:
0.00
AC:
0
AN:
39570
Gnomad4 SAS exome
AF:
0.0000584
AC:
5
AN:
85610
Gnomad4 FIN exome
AF:
0.00
AC:
0
AN:
53332
Gnomad4 NFE exome
AF:
0.0000144
AC:
16
AN:
1110298
Gnomad4 Remaining exome
AF:
0.00126
AC:
76
AN:
60218
Heterozygous variant carriers
0
41
81
122
162
203
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
30
60
90
120
150
<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:
0.00736
AC:
1119
AN:
152086
Hom.:
12
Cov.:
32
AF XY:
0.00683
AC XY:
508
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.0255
AC:
0.025523
AN:
0.025523
Gnomad4 AMR
AF:
0.00210
AC:
0.00209616
AN:
0.00209616
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 SAS
AF:
0.000207
AC:
0.000207383
AN:
0.000207383
Gnomad4 FIN
AF:
0.00
AC:
0
AN:
0
Gnomad4 NFE
AF:
0.000162
AC:
0.000161912
AN:
0.000161912
Gnomad4 OTH
AF:
0.00712
AC:
0.00711575
AN:
0.00711575
Heterozygous variant carriers
0
57
113
170
226
283
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<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:
0.000448
Hom.:
0
Bravo
AF:
0.00876
ESP6500AA
AF:
0.0275
AC:
121
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.00230
AC:
279
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.0000549
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Feb 26, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.53
D
Eigen
Uncertain
0.27
Eigen_PC
Benign
0.22
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.79
T
MetaRNN
Benign
0.013
T
MetaSVM
Benign
-0.51
T
MutationAssessor
Benign
1.6
L
PrimateAI
Benign
0.48
T
PROVEAN
Uncertain
-3.0
D
REVEL
Uncertain
0.35
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.046
D
Polyphen
1.0
D
Vest4
0.74
MVP
0.74
MPC
0.74
ClinPred
0.032
T
GERP RS
3.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.63
gMVP
0.78
Mutation Taster
=87/13
polymorphism

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: rs35004667; hg19: chr8-90785005; API