rs3843754

chr19-38316544-G-A

Variant summary

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

The ENST00000587039.1(YIF1B):c.-36+608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,908 control chromosomes in the GnomAD database, including 7,694 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 0.31 (7694 hom., cov: 31)
• Consequence: YIF1B ENST00000587039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YIF1B	XM_047439647.1	c.-36+608C>T		intron_variant
YIF1B	XM_047439648.1	c.-36+5284C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YIF1B	ENST00000587039.1	c.-36+608C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46809 AN: 151790 Hom.: 7683 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.309 AC: 46882 AN: 151908 Hom.: 7694 Cov.: 31 AF XY: 0.321 AC XY: 23833 AN XY: 74226

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.290

Alfa AF: 0.283 Hom.: 3812

Bravo AF: 0.307

Asia WGS AF: 0.449 AC: 1556 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	0.045
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3843754; hg19: chr19-38807184;