20-50645917-G-T

Variant names:

• chr20-50645917-G-T
• rs2426192
• NM_001290268.2:c.4-15061C>A

Variant summary

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

The NM_001290268.2(RIPOR3):​c.4-15061C>A 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 152,118 control chromosomes in the GnomAD database, including 9,963 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 (9957 hom., cov: 32)
  • Exomes 𝑓: 0.53 (6 hom.)
• Consequence: RIPOR3 NM_001290268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 5 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIPOR3	NM_001290268.2	c.4-15061C>A		intron_variant	Intron 1 of 21	ENST00000327979.8	NP_001277197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIPOR3	ENST00000327979.8	c.4-15061C>A		intron_variant	Intron 1 of 21	2	NM_001290268.2	ENSP00000332663.3
RIPOR3-AS1	ENST00000452336.1	n.212+31G>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51860 AN: 151966 Hom.: 9937 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.197

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: 0.531 AC: 17 AN: 32 Hom.: 6 Cov.: 0 AF XY: 0.462 AC XY: 12 AN XY: 26

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 12 AN: 24

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.342 AC: 51938 AN: 152086 Hom.: 9957 Cov.: 32 AF XY: 0.338 AC XY: 25137 AN XY: 74332

African (AFR) AF: 0.519 AC: 21543 AN: 41500

American (AMR) AF: 0.304 AC: 4646 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1097 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1019 AN: 5164

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4818

European-Finnish (FIN) AF: 0.295 AC: 3124 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18322 AN: 67982

Other (OTH) AF: 0.324 AC: 684 AN: 2112

Alfa AF: 0.295 Hom.: 21824

Bravo AF: 0.355

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.61
PhyloP100		-0.019
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: rs2426192; hg19: chr20-49262454;