rs13276910

chr8-89745593-T-G

Variant summary

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

The NR_125822.1(RIPK2-DT):n.667+11452A>C 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 0.249 in 152,182 control chromosomes in the GnomAD database, including 5,840 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 0.25 (5840 hom., cov: 32)
• Consequence: RIPK2-DT NR_125822.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPK2-DT	NR_125822.1	n.667+11452A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIPK2-DT	ENST00000688654.1	n.339+11452A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37923 AN: 152064 Hom.: 5838 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0413

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.249 AC: 37929 AN: 152182 Hom.: 5840 Cov.: 32 AF XY: 0.246 AC XY: 18283 AN XY: 74404

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0414

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.244

Alfa AF: 0.307 Hom.: 1689

Bravo AF: 0.236

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.2
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13276910; hg19: chr8-90757821;