Variant 21-41739855-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020639.3(RIPK4):c.*983G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,162 control chromosomes in the GnomAD database, including 11,107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 11099 hom., cov: 33)

Exomes 𝑓: 0.52 ( 8 hom. )

Consequence

RIPK4
NM_020639.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.98

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]

RIPK4 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 21-41739855-C-T is Benign according to our data. Variant chr21-41739855-C-T is described in ClinVar as [Benign]. Clinvar id is 339990.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIPK4	NM_020639.3 linkuse as main transcript	c.*983G>A		3_prime_UTR_variant	8/8	ENST00000332512.8	NP_065690.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPK4	ENST00000332512.8 linkuse as main transcript	c.*983G>A	3_prime_UTR_variant	8/8	1	NM_020639.3	ENSP00000332454	P1	P57078-2
	ENST00000423276.1 linkuse as main transcript	n.299+184C>T	intron_variant, non_coding_transcript_variant		3
RIPK4	ENST00000352483.3 linkuse as main transcript	c.*983G>A	3_prime_UTR_variant	9/9	5		ENSP00000330161		P57078-1

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56549

AN:

151994

Hom.:

11096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.412

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.404

GnomAD4 exome

AF:

0.520

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.667

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.372

AC:

56569

AN:

152112

Hom.:

11099

Cov.:

AF XY:

0.376

AC XY:

27937

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.408

Gnomad4 EAS

AF:

0.611

Gnomad4 SAS

AF:

0.393

Gnomad4 FIN

AF:

0.412

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.405

Alfa

AF:

0.403

Hom.:

12527

Bravo

AF:

0.372

Asia WGS

AF:

0.467

AC:

1621

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Bartsocas-Papas syndrome 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.43

DANN

Benign

0.24

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over