rs160441

chr8-89644760-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000688654.1(RIPK2-DT):n.498-48248A>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 0.553 in 152,102 control chromosomes in the GnomAD database, including 23,708 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 0.55 (23708 hom., cov: 33)
• Consequence: RIPK2-DT ENST00000688654.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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.498-48248A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84092 AN: 151984 Hom.: 23682 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.553 AC: 84167 AN: 152102 Hom.: 23708 Cov.: 33 AF XY: 0.561 AC XY: 41693 AN XY: 74332

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.585

Alfa AF: 0.573 Hom.: 28428

Bravo AF: 0.553

Asia WGS AF: 0.669 AC: 2326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
Cadd	Benign	15
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs160441; hg19: chr8-90656988;