20-50594416-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001290268.2(RIPOR3):c.2212+137C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,051,446 control chromosomes in the GnomAD database, including 40,644 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 0.23 (4780 hom., cov: 32)
  • Exomes 𝑓: 0.28 (35864 hom.)
• Consequence: RIPOR3 NM_001290268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.88

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPOR3	NM_001290268.2	c.2212+137C>G		intron_variant		ENST00000327979.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIPOR3	ENST00000327979.8	c.2212+137C>G		intron_variant		2	NM_001290268.2
RIPOR3	ENST00000045083.6	c.2200+137C>G		intron_variant		5		P1
RIPOR3	ENST00000482129.1	n.640+137C>G		intron_variant, non_coding_transcript_variant		3
RIPOR3	ENST00000488529.5	n.535+137C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35698 AN: 152034 Hom.: 4777 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.276 AC: 248153 AN: 899292 Hom.: 35864 AF XY: 0.274 AC XY: 123080 AN XY: 449518

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.288

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.180

Gnomad4 FIN exome AF: 0.292

Gnomad4 NFE exome AF: 0.297

Gnomad4 OTH exome AF: 0.261

GnomAD4 genome AF: 0.235 AC: 35713 AN: 152154 Hom.: 4780 Cov.: 32 AF XY: 0.234 AC XY: 17391 AN XY: 74376

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.228

Alfa AF: 0.263 Hom.: 746

Bravo AF: 0.228

Asia WGS AF: 0.152 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.46
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs914458; hg19: chr20-49210953; COSMIC: COSV50395460; COSMIC: COSV50395460;