8-89784141-TAAAAAAAAAAAAAAAA-TAAA

Position:

• chr8-89784141-TAAAAAAAAAAAAAAAA-TAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000220751.5(RIPK2):​c.1029+3_1029+15delAAAAAAAAAAAAA variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00000217 in 461,262 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: RIPK2 ENST00000220751.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIPK2	NM_003821.6	c.1029+13_1029+25delAAAAAAAAAAAAA		intron_variant		ENST00000220751.5	NP_003812.1
RIPK2	NM_001375360.1	c.618+13_618+25delAAAAAAAAAAAAA		intron_variant			NP_001362289.1
RIPK2	XM_011517357.3	c.516+13_516+25delAAAAAAAAAAAAA		intron_variant			XP_011515659.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPK2	ENST00000220751.5	c.1029+3_1029+15delAAAAAAAAAAAAA		splice_region_variant, intron_variant		1	NM_003821.6	ENSP00000220751.4
RIPK2	ENST00000522965.1	n.*668+3_*668+15delAAAAAAAAAAAAA		splice_region_variant, intron_variant		1		ENSP00000429271.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000217 AC: 1 AN: 461262 Hom.: 0 AF XY: 0.00000417 AC XY: 1 AN XY: 240056

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000386

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71268283; hg19: chr8-90796369;