20-50630793-C-A

Variant names:

• chr20-50630793-C-A
• rs141033220
• NM_001290268.2:c.67G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001290268.2(RIPOR3):​c.67G>T​(p.Val23Leu) variant causes a missense 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V23M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RIPOR3 NM_001290268.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21053603).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPOR3	NM_001290268.2	MANE Select	c.67G>T	p.Val23Leu	missense	Exon 2 of 22	NP_001277197.1	A0A499FJE4
	RIPOR3	NM_080829.4		c.55G>T	p.Val19Leu	missense	Exon 2 of 22	NP_543019.2	Q96MK2-1
	RIPOR3	NR_110890.2		n.666G>T		non_coding_transcript_exon	Exon 2 of 22

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPOR3	ENST00000327979.8	TSL:2 MANE Select	c.67G>T	p.Val23Leu	missense	Exon 2 of 22	ENSP00000332663.3	A0A499FJE4
	RIPOR3	ENST00000904044.1		c.67G>T	p.Val23Leu	missense	Exon 2 of 22	ENSP00000574103.1
	RIPOR3	ENST00000952575.1		c.67G>T	p.Val23Leu	missense	Exon 2 of 22	ENSP00000622634.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.049	T
Eigen	Benign	-0.30
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.30	N
LIST_S2	Benign	0.77	T
M_CAP	Benign	0.0070	T
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-1.1	T
PhyloP100		0.43
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.0070
Sift	Benign	0.072	T
Sift4G	Benign	0.14	T
Polyphen		0.40	B
Vest4		0.47
MVP		0.30
MPC		0.21
ClinPred		0.29	T
GERP RS		1.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.063
gMVP		0.26
Mutation Taster		=89/11	polymorphism

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: rs141033220; hg19: chr20-49247330;