20-50645619-T-C

Variant names:

• chr20-50645619-T-C
• rs2245361
• NM_001290268.2:c.4-14763A>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.4-14763A>G 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 152,658 control chromosomes in the GnomAD database, including 10,004 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 (9977 hom., cov: 32)
  • Exomes 𝑓: 0.26 (27 hom.)
• Consequence: RIPOR3 NM_001290268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIPOR3	NM_001290268.2	c.4-14763A>G		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.4-14763A>G		intron_variant	Intron 1 of 21	2	NM_001290268.2	ENSP00000332663.3
RIPOR3-AS1	ENST00000452336.1	n.24-79T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51906 AN: 151942 Hom.: 9957 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.198

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: 0.260 AC: 155 AN: 596 Hom.: 27 Cov.: 0 AF XY: 0.248 AC XY: 118 AN XY: 476

African (AFR) AF: 0.583 AC: 7 AN: 12

American (AMR) AF: 0.250 AC: 3 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.136 AC: 3 AN: 22

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AF: 0.333 AC: 2 AN: 6

European-Non Finnish (NFE) AF: 0.266 AC: 136 AN: 512

Other (OTH) AF: 0.200 AC: 4 AN: 20

GnomAD4 genome AF: 0.342 AC: 51984 AN: 152062 Hom.: 9977 Cov.: 32 AF XY: 0.338 AC XY: 25149 AN XY: 74320

African (AFR) AF: 0.520 AC: 21560 AN: 41466

American (AMR) AF: 0.304 AC: 4646 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5168

South Asian (SAS) AF: 0.231 AC: 1114 AN: 4816

European-Finnish (FIN) AF: 0.295 AC: 3122 AN: 10576

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

European-Non Finnish (NFE) AF: 0.270 AC: 18345 AN: 67982

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.304 Hom.: 7881

Bravo AF: 0.355

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.62
DANN	Benign	0.45
PhyloP100		-1.2
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: rs2245361; hg19: chr20-49262156;