rs16904179

Positions:

• chr8-129946705-G-A

Variant summary

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

The NM_001353258.2(CYRIB):​c.-137+24238C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0671 in 152,164 control chromosomes in the GnomAD database, including 530 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 0.067 (530 hom., cov: 32)
• Consequence: CYRIB NM_001353258.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYRIB	NM_001353258.2	c.-137+24238C>T		intron_variant		ENST00000694912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYRIB	ENST00000694912.1	c.-137+24238C>T		intron_variant			NM_001353258.2	P4
	ENST00000665358.1	n.64-1119G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0671 AC: 10198 AN: 152046 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0671 AC: 10203 AN: 152164 Hom.: 530 Cov.: 32 AF XY: 0.0702 AC XY: 5220 AN XY: 74390

Gnomad4 AFR AF: 0.0294

Gnomad4 AMR AF: 0.0728

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0673

Alfa AF: 0.0667 Hom.: 417

Bravo AF: 0.0639

Asia WGS AF: 0.204 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
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: rs16904179; hg19: chr8-130958951;