Variant chr6-83853366-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001009994.3(RIPPLY2):c.-51T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0734 in 1,486,130 control chromosomes in the GnomAD database, including 12,880 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 5252 hom., cov: 33)

Exomes 𝑓: 0.061 ( 7628 hom. )

Consequence

RIPPLY2
NM_001009994.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.230

Variant links:

Genes affected

RIPPLY2 (HGNC:21390): (ripply transcriptional repressor 2) This gene encodes a nuclear protein that belongs to a novel family of proteins required for vertebrate somitogenesis. Members of this family have a tetrapeptide WRPW motif that is required for interaction with the transcriptional repressor Groucho and a carboxy-terminal Ripply homology domain/Bowline-DSCR-Ledgerline conserved region required for transcriptional repression. Null mutant mice die soon after birth and display defects in axial skeleton segmentation due to defective somitogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

RIPPLY2 links:

ENSG00000287705 (HGNC:):

ENSG00000287705 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 6-83853366-T-C is Benign according to our data. Variant chr6-83853366-T-C is described in ClinVar as [Benign]. Clinvar id is 1247080.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
RIPPLY2	NM_001009994.3 linkuse as main transcript	c.-51T>C	5_prime_UTR_variant	1/4	ENST00000369689.6	NP_001009994.1	Q5TAB7-1
RIPPLY2	NM_001400900.1 linkuse as main transcript	c.-51T>C	5_prime_UTR_variant	1/3		NP_001387829.1
RIPPLY2-CYB5R4	NR_174604.1 linkuse as main transcript	n.7T>C	non_coding_transcript_exon_variant	1/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPPLY2	ENST00000369689 linkuse as main transcript	c.-51T>C		5_prime_UTR_variant	1/4	1	NM_001009994.3	ENSP00000358703.1		Q5TAB7-1
ENSG00000287705	ENST00000656981.1 linkuse as main transcript	n.802A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27741

AN:

152114

Hom.:

5229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.0572

Gnomad FIN

AF:

0.0525

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0346

Gnomad OTH

AF:

0.139

GnomAD3 exomes

AF:

0.131

AC:

16595

AN:

126248

Hom.:

2561

AF XY:

0.115

AC XY:

7948

AN XY:

69098

show subpopulations

Gnomad AFR exome

AF:

0.481

Gnomad AMR exome

AF:

0.329

Gnomad ASJ exome

AF:

0.0169

Gnomad EAS exome

AF:

0.272

Gnomad SAS exome

AF:

0.0551

Gnomad FIN exome

AF:

0.0534

Gnomad NFE exome

AF:

0.0344

Gnomad OTH exome

AF:

0.0855

GnomAD4 exome

AF:

0.0609

AC:

81287

AN:

1333898

Hom.:

7628

Cov.:

AF XY:

0.0588

AC XY:

38822

AN XY:

660470

show subpopulations

Gnomad4 AFR exome

AF:

0.480

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.0150

Gnomad4 EAS exome

AF:

0.239

Gnomad4 SAS exome

AF:

0.0543

Gnomad4 FIN exome

AF:

0.0562

Gnomad4 NFE exome

AF:

0.0353

Gnomad4 OTH exome

AF:

0.0853

GnomAD4 genome

AF:

0.183

AC:

27827

AN:

152232

Hom.:

5252

Cov.:

AF XY:

0.182

AC XY:

13581

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.459

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.0170

Gnomad4 EAS

AF:

0.267

Gnomad4 SAS

AF:

0.0574

Gnomad4 FIN

AF:

0.0525

Gnomad4 NFE

AF:

0.0346

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.0823

Hom.:

440

Bravo

AF:

0.214

Asia WGS

AF:

0.168

AC:

584

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.2

DANN

Benign

0.60

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