rs71268283

chr8-89784141-TAAAAAAAAAAAAAAAA-Tchr8-89784141-TAAAAAAAAAAAAAAAA-TAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_003821.6(RIPK2):c.1029+10_1029+25del variant causes a splice donor 5th base, 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. 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 splice_donor_5th_base, 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd at 26 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPK2	NM_003821.6	c.1029+10_1029+25del		splice_donor_5th_base_variant, intron_variant		ENST00000220751.5
RIPK2	NM_001375360.1	c.618+10_618+25del		splice_donor_5th_base_variant, intron_variant
RIPK2	XM_011517357.3	c.516+10_516+25del		splice_donor_5th_base_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIPK2	ENST00000220751.5	c.1029+10_1029+25del		splice_donor_5th_base_variant, intron_variant		1	NM_003821.6	P1
RIPK2	ENST00000522965.1	c.*668+10_*668+25del		splice_donor_5th_base_variant, intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.000268 AC: 26 AN: 97062 Hom.: 0 Cov.: 0

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

Gnomad4 AFR exome AF: 0.00137

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.000134

GnomAD4 genome AF: 0.000268 AC: 26 AN: 97070 Hom.: 0 Cov.: 0 AF XY: 0.000249 AC XY: 11 AN XY: 44206

Gnomad4 AFR AF: 0.00111

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;