rs4312417

chr19-38306549-A-G

Variant summary

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

The NM_001039672.3(YIF1B):c.789+879T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 162,756 control chromosomes in the GnomAD database, including 8,729 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 0.32 (8164 hom., cov: 32)
  • Exomes 𝑓: 0.29 (565 hom.)
• Consequence: YIF1B NM_001039672.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

Genes affected

YIF1B (HGNC:30511): (Yip1 interacting factor homolog B, membrane trafficking protein) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein targeting to membrane; and sperm axoneme assembly. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YIF1B	NM_001039672.3	c.789+879T>C		intron_variant		ENST00000339413.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YIF1B	ENST00000339413.11	c.789+879T>C		intron_variant		1	NM_001039672.3	P3

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47842 AN: 151854 Hom.: 8144 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.289 AC: 3121 AN: 10784 Hom.: 565 AF XY: 0.298 AC XY: 1727 AN XY: 5800

Gnomad4 AFR exome AF: 0.385

Gnomad4 AMR exome AF: 0.388

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.591

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.238

Gnomad4 OTH exome AF: 0.242

GnomAD4 genome AF: 0.315 AC: 47925 AN: 151972 Hom.: 8164 Cov.: 32 AF XY: 0.329 AC XY: 24442 AN XY: 74286

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.292

Alfa AF: 0.291 Hom.: 2516

Bravo AF: 0.314

Asia WGS AF: 0.496 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.36

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

Publications

LitVar

Other links and lift over

dbSNP: rs4312417; hg19: chr19-38797189;