rs218949

chr8-89708239-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688654.1(RIPK2-DT):n.497+6185A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,056 control chromosomes in the GnomAD database, including 7,002 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7002 hom., cov: 32)
• Consequence: RIPK2-DT ENST00000688654.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

RIPK2-DT (HGNC:55545): (palmitic acid regulated anti-inflammatory lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIPK2-DT	ENST00000688654.1	n.497+6185A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42299 AN: 151938 Hom.: 6998 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0424

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.278 AC: 42314 AN: 152056 Hom.: 7002 Cov.: 32 AF XY: 0.271 AC XY: 20156 AN XY: 74304

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.269

Alfa AF: 0.338 Hom.: 1191

Bravo AF: 0.267

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.9
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs218949; hg19: chr8-90720467;