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: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587039.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIF1B	ENST00000587039.1	TSL:5	c.-36+608C>T		intron	N/A	ENSP00000465277.1	K7EJQ6

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3843754;

hg19: chr19-38807184;