8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAA

Position:

• chr8-89784141-TAAAAAAAAAAAAAAAA-TAAAAAAAA

Variant summary

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

The NM_003821.6(RIPK2):​c.1029+18_1029+25delAAAAAAAA variant causes a intron change. The variant allele was found at a frequency of 0.00187 in 556,984 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 0.00015 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0022 (0 hom.)
• Consequence: RIPK2 NM_003821.6 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 GnomAd4 at 15 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIPK2	NM_003821.6	c.1029+18_1029+25delAAAAAAAA		intron_variant		ENST00000220751.5	NP_003812.1
RIPK2	NM_001375360.1	c.618+18_618+25delAAAAAAAA		intron_variant			NP_001362289.1
RIPK2	XM_011517357.3	c.516+18_516+25delAAAAAAAA		intron_variant			XP_011515659.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPK2	ENST00000220751.5	c.1029+18_1029+25delAAAAAAAA		intron_variant		1	NM_003821.6	ENSP00000220751.4
RIPK2	ENST00000522965.1	n.*668+18_*668+25delAAAAAAAA		intron_variant		1		ENSP00000429271.1

Frequencies

GnomAD3 genomes AF: 0.000155 AC: 15 AN: 97064 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000427

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00107

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00450

Gnomad NFE AF: 0.000174

Gnomad OTH AF: 0.000780

GnomAD4 exome AF: 0.00223 AC: 1024 AN: 459912 Hom.: 0 AF XY: 0.00224 AC XY: 536 AN XY: 239288

Gnomad4 AFR exome AF: 0.00179

Gnomad4 AMR exome AF: 0.00291

Gnomad4 ASJ exome AF: 0.00254

Gnomad4 EAS exome AF: 0.000145

Gnomad4 SAS exome AF: 0.00143

Gnomad4 FIN exome AF: 0.00162

Gnomad4 NFE exome AF: 0.00245

Gnomad4 OTH exome AF: 0.00224

GnomAD4 genome AF: 0.000155 AC: 15 AN: 97072 Hom.: 0 Cov.: 0 AF XY: 0.000181 AC XY: 8 AN XY: 44206

Gnomad4 AFR AF: 0.0000426

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00107

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000174

Gnomad4 OTH AF: 0.000774

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;