19-38307446-T-C

Variant names:

• chr19-38307446-T-C
• rs3178327
• NM_001039672.3:c.771A>G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001039672.3(YIF1B):​c.771A>G​(p.Val257Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 1,613,022 control chromosomes in the GnomAD database, including 75,740 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 0.29 (6836 hom., cov: 30)
  • Exomes 𝑓: 0.30 (68904 hom.)
• Consequence: YIF1B NM_001039672.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP7: Synonymous conserved (PhyloP=-0.071 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIF1B	NM_001039672.3	c.771A>G	p.Val257Val	synonymous_variant	Exon 7 of 8	ENST00000339413.11	NP_001034761.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIF1B	ENST00000339413.11	c.771A>G	p.Val257Val	synonymous_variant	Exon 7 of 8	1	NM_001039672.3	ENSP00000343435.5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43153 AN: 151474 Hom.: 6825 Cov.: 30

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.268

GnomAD3 exomes AF: 0.344 AC: 85870 AN: 249862 Hom.: 16288 AF XY: 0.341 AC XY: 46136 AN XY: 135312

Gnomad AFR exome AF: 0.181

Gnomad AMR exome AF: 0.469

Gnomad ASJ exome AF: 0.292

Gnomad EAS exome AF: 0.547

Gnomad SAS exome AF: 0.398

Gnomad FIN exome AF: 0.413

Gnomad NFE exome AF: 0.273

Gnomad OTH exome AF: 0.326

GnomAD4 exome AF: 0.298 AC: 435313 AN: 1461428 Hom.: 68904 Cov.: 37 AF XY: 0.300 AC XY: 218378 AN XY: 727000

Gnomad4 AFR exome AF: 0.183

Gnomad4 AMR exome AF: 0.469

Gnomad4 ASJ exome AF: 0.292

Gnomad4 EAS exome AF: 0.547

Gnomad4 SAS exome AF: 0.391

Gnomad4 FIN exome AF: 0.405

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.285 AC: 43215 AN: 151594 Hom.: 6836 Cov.: 30 AF XY: 0.298 AC XY: 22089 AN XY: 74058

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.270

Alfa AF: 0.278 Hom.: 8436

Bravo AF: 0.280

Asia WGS AF: 0.445 AC: 1543 AN: 3478

EpiCase AF: 0.272

EpiControl AF: 0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.66
RBP_binding_hub_radar		1.0
RBP_regulation_power_radar		2.9

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: rs3178327; hg19: chr19-38798086; COSMIC: COSV56650288; COSMIC: COSV56650288;