Genetic Variant YIF1B:p.Val257Val (chr19-38307446-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710

Publications

24 publications found

Variant links:

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

YIF1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	c.771A>G	p.Val257Val	synonymous_variant	Exon 7 of 8	ENST00000339413.11	NP_001034761.1	Q5BJH7-1Q9H5F7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIF1B	ENST00000339413.11 link	c.771A>G	p.Val257Val	synonymous_variant	Exon 7 of 8	1	NM_001039672.3	ENSP00000343435.5		Q5BJH7-1

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43153

AN:

151474

Hom.:

6825

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.344

AC:

85870

AN:

249862

AF XY:

0.341

show subpopulations

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 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.:

AF XY:

0.300

AC XY:

218378

AN XY:

727000

show subpopulations

African (AFR)

AF:

0.183

AC:

6124

AN:

33480

American (AMR)

AF:

0.469

AC:

20931

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.292

AC:

7641

AN:

26134

East Asian (EAS)

AF:

0.547

AC:

21725

AN:

39692

South Asian (SAS)

AF:

0.391

AC:

33753

AN:

86246

European-Finnish (FIN)

AF:

0.405

AC:

21552

AN:

53196

Middle Eastern (MID)

AF:

0.304

AC:

1755

AN:

5768

European-Non Finnish (NFE)

AF:

0.273

AC:

303461

AN:

1111868

Other (OTH)

AF:

0.304

AC:

18371

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

17694

35388

53083

70777

88471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.285

AC:

43215

AN:

151594

Hom.:

6836

Cov.:

AF XY:

0.298

AC XY:

22089

AN XY:

74058

show subpopulations

African (AFR)

AF:

0.185

AC:

7633

AN:

41364

American (AMR)

AF:

0.391

AC:

5940

AN:

15190

Ashkenazi Jewish (ASJ)

AF:

0.295

AC:

1023

AN:

3472

East Asian (EAS)

AF:

0.561

AC:

2870

AN:

5120

South Asian (SAS)

AF:

0.397

AC:

1911

AN:

4808

European-Finnish (FIN)

AF:

0.431

AC:

4516

AN:

10482

Middle Eastern (MID)

AF:

0.257

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.273

AC:

18504

AN:

67856

Other (OTH)

AF:

0.270

AC:

568

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1508

3016

4523

6031

7539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.279

Hom.:

10746

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

(source)

DANN

Benign

0.66

PhyloP100

-0.071

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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chr19-38307446-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over