rs55860816

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020639.3(RIPK4):​c.182+660C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,154 control chromosomes in the GnomAD database, including 6,394 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 ( 6394 hom., cov: 33)

Consequence

RIPK4
NM_020639.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.286
Variant links:
Genes affected
RIPK4 (HGNC:496): (receptor interacting serine/threonine kinase 4) The protein encoded by this gene is a serine/threonine protein kinase that interacts with protein kinase C-delta. The encoded protein can also activate NFkappaB and is required for keratinocyte differentiation. This kinase undergoes autophosphorylation. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RIPK4NM_020639.3 linkuse as main transcriptc.182+660C>T intron_variant ENST00000332512.8 NP_065690.2 Q9H4D1Q96T11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RIPK4ENST00000332512.8 linkuse as main transcriptc.182+660C>T intron_variant 1 NM_020639.3 ENSP00000332454.3 P57078-2
RIPK4ENST00000352483.3 linkuse as main transcriptc.182+660C>T intron_variant 5 ENSP00000330161.2 P57078-1

Frequencies

GnomAD3 genomes
AF:
0.280
AC:
42499
AN:
152034
Hom.:
6394
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.363
Gnomad AMI
AF:
0.192
Gnomad AMR
AF:
0.221
Gnomad ASJ
AF:
0.264
Gnomad EAS
AF:
0.0354
Gnomad SAS
AF:
0.242
Gnomad FIN
AF:
0.197
Gnomad MID
AF:
0.260
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.279
AC:
42521
AN:
152154
Hom.:
6394
Cov.:
33
AF XY:
0.271
AC XY:
20132
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.362
Gnomad4 AMR
AF:
0.221
Gnomad4 ASJ
AF:
0.264
Gnomad4 EAS
AF:
0.0349
Gnomad4 SAS
AF:
0.242
Gnomad4 FIN
AF:
0.197
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.268
Alfa
AF:
0.283
Hom.:
812
Bravo
AF:
0.283
Asia WGS
AF:
0.155
AC:
543
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
3.8
DANN
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs55860816; hg19: chr21-43186360; API