Variant chr20-50645619-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001290268.2(RIPOR3):c.4-14763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,658 control chromosomes in the GnomAD database, including 10,004 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 ( 9977 hom., cov: 32)

Exomes 𝑓: 0.26 ( 27 hom. )

Consequence

RIPOR3
NM_001290268.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

RIPOR3 (HGNC:16168): (RIPOR family member 3)

RIPOR3 links:

RIPOR3-AS1 (HGNC:40760): (RIPOR3 antisense RNA 1)

RIPOR3-AS1 links:

Genome browser will be placed here

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 = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPOR3	NM_001290268.2 linkuse as main transcript	c.4-14763A>G		intron_variant		ENST00000327979.8
RIPOR3-AS1	NR_111906.1 linkuse as main transcript	n.24-79T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIPOR3	ENST00000327979.8 linkuse as main transcript	c.4-14763A>G		intron_variant		2	NM_001290268.2
RIPOR3-AS1	ENST00000452336.1 linkuse as main transcript	n.24-79T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

51906

AN:

151942

Hom.:

9957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.520

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.321

GnomAD4 exome

AF:

0.260

AC:

155

AN:

596

Hom.:

Cov.:

AF XY:

0.248

AC XY:

118

AN XY:

476

show subpopulations

Gnomad4 AFR exome

AF:

0.583

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.266

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.342

AC:

51984

AN:

152062

Hom.:

9977

Cov.:

AF XY:

0.338

AC XY:

25149

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.520

Gnomad4 AMR

AF:

0.304

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.324

Alfa

AF:

0.292

Hom.:

5547

Bravo

AF:

0.355

Asia WGS

AF:

0.270

AC:

942

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

0.62

DANN

Benign

0.45

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over