rs2060983

chr8-130012788-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001353258.2(CYRIB):c.-190+3582G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,990 control chromosomes in the GnomAD database, including 15,259 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 0.44 (15259 hom., cov: 32)
• Consequence: CYRIB NM_001353258.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

CYRIB (HGNC:25216): (CYFIP related Rac1 interactor B) Enables small GTPase binding activity. Involved in several processes, including cellular response to molecule of bacterial origin; negative regulation of small GTPase mediated signal transduction; and regulation of organelle organization. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYRIB	NM_001353258.2	c.-190+3582G>A		intron_variant		ENST00000694912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYRIB	ENST00000694912.1	c.-190+3582G>A		intron_variant			NM_001353258.2	P4

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67365 AN: 151874 Hom.: 15231 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.444 AC: 67432 AN: 151990 Hom.: 15259 Cov.: 32 AF XY: 0.444 AC XY: 32999 AN XY: 74278

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.453

Alfa AF: 0.418 Hom.: 18982

Bravo AF: 0.456

Asia WGS AF: 0.506 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.86
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2060983; hg19: chr8-131025034;