chr8-89784141-TAAAAAAAAAAAAA-T

Variant names:

• chr8-89784141-TAAAAAAAAAAAAA-T
• rs71268283
• NM_003821.6:c.1029+13_1029+25delAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Publications: 0 publications found

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]

PARAIL (HGNC:55545): (palmitic acid regulated anti-inflammatory lncRNA)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000220751.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPK2	NM_003821.6	MANE Select	c.1029+13_1029+25delAAAAAAAAAAAAA		intron	N/A	NP_003812.1	O43353-1
	RIPK2	NM_001375360.1		c.618+13_618+25delAAAAAAAAAAAAA		intron	N/A	NP_001362289.1	O43353-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPK2	ENST00000220751.5	TSL:1 MANE Select	c.1029+3_1029+15delAAAAAAAAAAAAA		splice_region intron	N/A	ENSP00000220751.4	O43353-1
	RIPK2	ENST00000522965.1	TSL:1	n.*668+3_*668+15delAAAAAAAAAAAAA		splice_region intron	N/A	ENSP00000429271.1	E7ERW9
	RIPK2	ENST00000929530.1		c.1089+3_1089+15delAAAAAAAAAAAAA		splice_region intron	N/A	ENSP00000599589.1

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

African (AFR) AF: 0.00 AC: 0 AN: 9520

American (AMR) AF: 0.00 AC: 0 AN: 11044

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10276

East Asian (EAS) AF: 0.00 AC: 0 AN: 20676

South Asian (SAS) AF: 0.0000386 AC: 1 AN: 25888

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28494

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1686

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 331324

Other (OTH) AF: 0.00 AC: 0 AN: 22354

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs71268283; hg19: chr8-90796369; COSMIC: COSV55132733; COSMIC: COSV55132733;