20-50594416-G-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001290268.2(RIPOR3):​c.2212+137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001290268.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPOR3	NM_001290268.2	MANE Select	c.2212+137C>T		intron	N/A	NP_001277197.1
	RIPOR3	NM_080829.4		c.2200+137C>T		intron	N/A	NP_543019.2
	RIPOR3	NR_110890.2		n.2785+137C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPOR3	ENST00000327979.8	TSL:2 MANE Select	c.2212+137C>T		intron	N/A	ENSP00000332663.3
	RIPOR3	ENST00000045083.6	TSL:5	c.2200+137C>T		intron	N/A	ENSP00000045083.2
	RIPOR3	ENST00000482129.1	TSL:3	n.640+137C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.53
DANN	Benign	0.94
PhyloP100		-5.9

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;