20-50594416-G-C

Variant names:

• chr20-50594416-G-C
• rs914458
• NM_001290268.2:c.2212+137C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RIPOR3	NM_001290268.2	c.2212+137C>G		intron_variant	Intron 17 of 21	ENST00000327979.8	NP_001277197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIPOR3	ENST00000327979.8	c.2212+137C>G		intron_variant	Intron 17 of 21	2	NM_001290268.2	ENSP00000332663.3
RIPOR3	ENST00000045083.6	c.2200+137C>G		intron_variant	Intron 17 of 21	5		ENSP00000045083.2
RIPOR3	ENST00000482129.1	n.640+137C>G		intron_variant	Intron 1 of 2	3
RIPOR3	ENST00000488529.5	n.535+137C>G		intron_variant	Intron 4 of 6	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

African (AFR) AF: 0.114 AC: 2433 AN: 21400

American (AMR) AF: 0.236 AC: 5886 AN: 24922

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 4570 AN: 15870

East Asian (EAS) AF: 0.127 AC: 4466 AN: 35150

South Asian (SAS) AF: 0.180 AC: 8795 AN: 48826

European-Finnish (FIN) AF: 0.292 AC: 12725 AN: 43560

Middle Eastern (MID) AF: 0.248 AC: 769 AN: 3098

European-Non Finnish (NFE) AF: 0.297 AC: 198077 AN: 666568

Other (OTH) AF: 0.261 AC: 10432 AN: 39898

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

African (AFR) AF: 0.118 AC: 4895 AN: 41530

American (AMR) AF: 0.259 AC: 3969 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3472

East Asian (EAS) AF: 0.127 AC: 656 AN: 5172

South Asian (SAS) AF: 0.175 AC: 841 AN: 4814

European-Finnish (FIN) AF: 0.293 AC: 3100 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20378 AN: 67978

Other (OTH) AF: 0.228 AC: 481 AN: 2114

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
PhyloP100		-5.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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