rs2245361

Positions:

• chr20-50645619-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

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

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

ACMG classification

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	c.4-14763A>G		intron_variant		ENST00000327979.8
RIPOR3-AS1	NR_111906.1	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	c.4-14763A>G		intron_variant		2	NM_001290268.2
RIPOR3-AS1	ENST00000452336.1	n.24-79T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51906 AN: 151942 Hom.: 9957 Cov.: 32

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.: 27 Cov.: 0 AF XY: 0.248 AC XY: 118 AN XY: 476

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.: 32 AF XY: 0.338 AC XY: 25149 AN XY: 74320

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

Other links and lift over

dbSNP: rs2245361; hg19: chr20-49262156;