8-89784141-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003821.6(RIPK2):​c.1029+25dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 5283 hom., cov: 0)
Exomes 𝑓: 0.075 ( 11 hom. )

Consequence

RIPK2
NM_003821.6 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.604
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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 8-89784141-T-TA is Benign according to our data. Variant chr8-89784141-T-TA is described in ClinVar as [Benign]. Clinvar id is 2867178.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RIPK2NM_003821.6 linkuse as main transcriptc.1029+25dup splice_region_variant, intron_variant ENST00000220751.5 NP_003812.1
RIPK2NM_001375360.1 linkuse as main transcriptc.618+25dup splice_region_variant, intron_variant NP_001362289.1
RIPK2XM_011517357.3 linkuse as main transcriptc.516+25dup splice_region_variant, intron_variant XP_011515659.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RIPK2ENST00000220751.5 linkuse as main transcriptc.1029+25dup splice_region_variant, intron_variant 1 NM_003821.6 ENSP00000220751 P1O43353-1
RIPK2ENST00000522965.1 linkuse as main transcriptc.*668+25dup splice_region_variant, intron_variant, NMD_transcript_variant 1 ENSP00000429271

Frequencies

GnomAD3 genomes
AF:
0.324
AC:
31322
AN:
96572
Hom.:
5282
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.519
Gnomad AMR
AF:
0.408
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.436
Gnomad SAS
AF:
0.452
Gnomad FIN
AF:
0.261
Gnomad MID
AF:
0.273
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.327
GnomAD3 exomes
AF:
0.0323
AC:
925
AN:
28604
Hom.:
19
AF XY:
0.0305
AC XY:
463
AN XY:
15204
show subpopulations
Gnomad AFR exome
AF:
0.0380
Gnomad AMR exome
AF:
0.0782
Gnomad ASJ exome
AF:
0.0489
Gnomad EAS exome
AF:
0.0809
Gnomad SAS exome
AF:
0.0460
Gnomad FIN exome
AF:
0.00254
Gnomad NFE exome
AF:
0.0215
Gnomad OTH exome
AF:
0.0441
GnomAD4 exome
AF:
0.0750
AC:
33709
AN:
449438
Hom.:
11
Cov.:
0
AF XY:
0.0754
AC XY:
17632
AN XY:
233904
show subpopulations
Gnomad4 AFR exome
AF:
0.0452
Gnomad4 AMR exome
AF:
0.0882
Gnomad4 ASJ exome
AF:
0.107
Gnomad4 EAS exome
AF:
0.130
Gnomad4 SAS exome
AF:
0.104
Gnomad4 FIN exome
AF:
0.0538
Gnomad4 NFE exome
AF:
0.0704
Gnomad4 OTH exome
AF:
0.0784
GnomAD4 genome
AF:
0.324
AC:
31320
AN:
96586
Hom.:
5283
Cov.:
0
AF XY:
0.320
AC XY:
14085
AN XY:
43948
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.409
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.436
Gnomad4 SAS
AF:
0.452
Gnomad4 FIN
AF:
0.261
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.327

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 08, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs71268283; hg19: chr8-90796369; API