8-89784141-TAAAAAAAAAAA-T

Position:

• chr8-89784141-TAAAAAAAAAAA-T

Variant summary

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

The NM_003821.6(RIPK2):​c.1029+15_1029+25delAAAAAAAAAAA variant causes a intron change. The variant allele was found at a frequency of 0.000435 in 558,286 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00026 (2 hom., cov: 0)
  • Exomes 𝑓: 0.00047 (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 25 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIPK2	NM_003821.6	c.1029+15_1029+25delAAAAAAAAAAA		intron_variant		ENST00000220751.5	NP_003812.1
RIPK2	NM_001375360.1	c.618+15_618+25delAAAAAAAAAAA		intron_variant			NP_001362289.1
RIPK2	XM_011517357.3	c.516+15_516+25delAAAAAAAAAAA		intron_variant			XP_011515659.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPK2	ENST00000220751.5	c.1029+15_1029+25delAAAAAAAAAAA		intron_variant		1	NM_003821.6	ENSP00000220751.4
RIPK2	ENST00000522965.1	n.*668+15_*668+25delAAAAAAAAAAA		intron_variant		1		ENSP00000429271.1

Frequencies

GnomAD3 genomes AF: 0.000258 AC: 25 AN: 97064 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.0000427

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00664

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000383

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000773

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000473 AC: 218 AN: 461214 Hom.: 0 AF XY: 0.000458 AC XY: 110 AN XY: 240026

Gnomad4 AFR exome AF: 0.000105

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00929

Gnomad4 SAS exome AF: 0.000270

Gnomad4 FIN exome AF: 0.0000702

Gnomad4 NFE exome AF: 0.0000392

Gnomad4 OTH exome AF: 0.000134

GnomAD4 genome AF: 0.000258 AC: 25 AN: 97072 Hom.: 2 Cov.: 0 AF XY: 0.000339 AC XY: 15 AN XY: 44206

Gnomad4 AFR AF: 0.0000426

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00665

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000383

Gnomad4 NFE AF: 0.0000773

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;