NM_015653.5:c.*304G>A

Variant names:

• chr22-45432666-G-A
• rs11913200
• NM_015653.5:c.*304G>A

Variant summary

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

The NM_015653.5(RIBC2):​c.*304G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,112 control chromosomes in the GnomAD database, including 6,601 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 0.27 (6601 hom., cov: 33)
• Consequence: RIBC2 NM_015653.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 9 publications found

Genes affected

RIBC2 (HGNC:13241): (RIB43A domain with coiled-coils 2) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIBC2	NM_015653.5	c.*304G>A		downstream_gene_variant		ENST00000614167.2	NP_056468.3
RIBC2	XM_005261524.5	c.*304G>A		downstream_gene_variant			XP_005261581.1
RIBC2	XM_011530126.3	c.*304G>A		downstream_gene_variant			XP_011528428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIBC2	ENST00000614167.2	c.*304G>A		downstream_gene_variant		1	NM_015653.5	ENSP00000483356.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41725 AN: 151994 Hom.: 6582 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.275 AC: 41796 AN: 152112 Hom.: 6601 Cov.: 33 AF XY: 0.275 AC XY: 20464 AN XY: 74362

African (AFR) AF: 0.418 AC: 17324 AN: 41488

American (AMR) AF: 0.229 AC: 3498 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1942 AN: 5174

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4818

European-Finnish (FIN) AF: 0.229 AC: 2416 AN: 10564

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13735 AN: 67980

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.229 Hom.: 11447

Bravo AF: 0.279

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.54
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11913200; hg19: chr22-45828546;