chr20-50588558-G-A

Variant names:

• chr20-50588558-G-A
• rs1060402
• NM_001290268.2:c.2662-666C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001290268.2(RIPOR3):​c.2662-666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,858 control chromosomes in the GnomAD database, including 16,813 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 0.46 (16813 hom., cov: 32)
• Consequence: RIPOR3 NM_001290268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 12 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIPOR3	NM_001290268.2	c.2662-666C>T		intron_variant	Intron 20 of 21	ENST00000327979.8	NP_001277197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIPOR3	ENST00000327979.8	c.2662-666C>T		intron_variant	Intron 20 of 21	2	NM_001290268.2	ENSP00000332663.3
RIPOR3	ENST00000045083.6	c.2650-666C>T		intron_variant	Intron 20 of 21	5		ENSP00000045083.2
RIPOR3	ENST00000462842.1	n.328-666C>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69697 AN: 151744 Hom.: 16814 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.459 AC: 69712 AN: 151858 Hom.: 16813 Cov.: 32 AF XY: 0.462 AC XY: 34283 AN XY: 74208

African (AFR) AF: 0.298 AC: 12353 AN: 41394

American (AMR) AF: 0.473 AC: 7218 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1850 AN: 3466

East Asian (EAS) AF: 0.623 AC: 3209 AN: 5154

South Asian (SAS) AF: 0.607 AC: 2922 AN: 4816

European-Finnish (FIN) AF: 0.540 AC: 5677 AN: 10518

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34748 AN: 67932

Other (OTH) AF: 0.485 AC: 1023 AN: 2108

Alfa AF: 0.496 Hom.: 10093

Bravo AF: 0.447

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		0.10
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: rs1060402; hg19: chr20-49205095;