rs160441

Variant names:

• chr8-89644760-T-C
• rs160441
• ENST00000688855.1:n.948A>G

Variant summary

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

The ENST00000688855.1(RIPK2-DT):​n.948A>G variant causes a non coding transcript exon 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 ENST00000688855.1 non_coding_transcript_exon
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIPK2-DT	ENST00000688855.1	n.948A>G		non_coding_transcript_exon_variant	Exon 3 of 3
RIPK2-DT	ENST00000519655.6	n.684-15489A>G		intron_variant	Intron 1 of 6	5
RIPK2-DT	ENST00000524190.2	n.340-15509A>G		intron_variant	Intron 1 of 3	3

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;