21-41740054-A-ACT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_020639.3(RIPK4):c.*783_*784insAG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (13192 hom., cov: 0)
  • Exomes 𝑓: 0.40 (0 hom.)
• Consequence: RIPK4 NM_020639.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.113

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 21-41740054-A-ACT is Benign according to our data. Variant chr21-41740054-A-ACT is described in ClinVar as [Benign]. Clinvar id is 339992.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPK4	NM_020639.3	c.*783_*784insAG		3_prime_UTR_variant	8/8	ENST00000332512.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIPK4	ENST00000332512.8	c.*783_*784insAG		3_prime_UTR_variant	8/8	1	NM_020639.3	P1
	ENST00000423276.1	n.299+384_299+385dup		intron_variant, non_coding_transcript_variant		3
RIPK4	ENST00000352483.3	c.*783_*784insAG		3_prime_UTR_variant	9/9	5

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61668 AN: 151696 Hom.: 13192 Cov.: 0

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.400 AC: 4 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.406 AC: 61684 AN: 151814 Hom.: 13192 Cov.: 0 AF XY: 0.410 AC XY: 30413 AN XY: 74184

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.439

Alfa AF: 0.417 Hom.: 1647

Bravo AF: 0.403

Asia WGS AF: 0.472 AC: 1640 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Popliteal pterygium syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34075882; hg19: chr21-43160214;