8-89626244-C-G

Variant names:

• chr8-89626244-C-G
• rs4961149
• ENST00000519655.6:n.946+1911G>C

Variant summary

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

The ENST00000524190.2(RIPK2-DT):​n.582+1911G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,998 control chromosomes in the GnomAD database, including 10,905 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 0.34 (10905 hom., cov: 32)
• Consequence: RIPK2-DT ENST00000524190.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770

Genes affected

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

LOC112268015 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268015	XR_002956661.2	n.2590+226G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIPK2-DT	ENST00000519655.6	n.946+1911G>C		intron_variant	Intron 3 of 6	5
RIPK2-DT	ENST00000524190.2	n.582+1911G>C		intron_variant	Intron 3 of 3	3
RIPK2-DT	ENST00000656898.2	n.802-14255G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51817 AN: 151880 Hom.: 10896 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.341 AC: 51844 AN: 151998 Hom.: 10905 Cov.: 32 AF XY: 0.352 AC XY: 26160 AN XY: 74286

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.360

Alfa AF: 0.243 Hom.: 641

Bravo AF: 0.330

Asia WGS AF: 0.556 AC: 1933 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961149; hg19: chr8-90638473;