rs3843754

Variant names:

• chr19-38316544-G-A
• rs3843754
• ENST00000587039.1:c.-36+608C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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]

YIF1B Gene-Disease associations (from GenCC):

• Kaya-Barakat-Masson syndrome

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
YIF1B	XM_047439647.1	c.-36+608C>T		intron_variant	Intron 1 of 7		XP_047295603.1
YIF1B	XM_047439648.1	c.-36+5284C>T		intron_variant	Intron 1 of 7		XP_047295604.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIF1B	ENST00000587039.1	c.-36+608C>T		intron_variant	Intron 1 of 2	5		ENSP00000465277.1

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

African (AFR) AF: 0.268 AC: 11087 AN: 41424

American (AMR) AF: 0.400 AC: 6099 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2894 AN: 5162

South Asian (SAS) AF: 0.396 AC: 1907 AN: 4820

European-Finnish (FIN) AF: 0.430 AC: 4530 AN: 10524

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18474 AN: 67950

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.288 Hom.: 6812

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs3843754; hg19: chr19-38807184;