Genetic Variant YIF1B:c.789+879T>C (chr19-38306549-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001039672.3(YIF1B):c.789+879T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 162,756 control chromosomes in the GnomAD database, including 8,729 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 0.32 ( 8164 hom., cov: 32)

Exomes 𝑓: 0.29 ( 565 hom. )

Consequence

YIF1B
NM_001039672.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.319

Publications

11 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039672.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
YIF1B	NM_001039672.3	MANE Select	c.789+879T>C	intron	N/A	NP_001034761.1
YIF1B	NM_001039673.3		c.780+879T>C	intron	N/A	NP_001034762.1
YIF1B	NM_001039671.3		c.744+879T>C	intron	N/A	NP_001034760.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
YIF1B	ENST00000339413.11	TSL:1 MANE Select	c.789+879T>C	intron	N/A	ENSP00000343435.5
YIF1B	ENST00000337679.12	TSL:1	c.857+365T>C	intron	N/A	ENSP00000337411.7
YIF1B	ENST00000392124.7	TSL:1	c.696+879T>C	intron	N/A	ENSP00000375971.2

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47842

AN:

151854

Hom.:

8144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.289

GnomAD4 exome

AF:

0.289

AC:

3121

AN:

10784

Hom.:

565

AF XY:

0.298

AC XY:

1727

AN XY:

5800

show subpopulations

African (AFR)

AF:

0.385

AC:

AN:

American (AMR)

AF:

0.388

AC:

627

AN:

1614

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.591

AC:

AN:

South Asian (SAS)

AF:

0.389

AC:

643

AN:

1652

European-Finnish (FIN)

AF:

0.331

AC:

AN:

260

Middle Eastern (MID)

AF:

0.269

AC:

AN:

European-Non Finnish (NFE)

AF:

0.238

AC:

1553

AN:

6530

Other (OTH)

AF:

0.242

AC:

119

AN:

492

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

108

217

325

434

542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.315

AC:

47925

AN:

151972

Hom.:

8164

Cov.:

AF XY:

0.329

AC XY:

24442

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.277

AC:

11475

AN:

41444

American (AMR)

AF:

0.400

AC:

6098

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

1036

AN:

3464

East Asian (EAS)

AF:

0.630

AC:

3249

AN:

5160

South Asian (SAS)

AF:

0.430

AC:

2069

AN:

4808

European-Finnish (FIN)

AF:

0.431

AC:

4559

AN:

10574

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.273

AC:

18567

AN:

67960

Other (OTH)

AF:

0.292

AC:

616

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1628

3255

4883

6510

8138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.290

Hom.:

3838

Bravo

AF:

0.314

Asia WGS

AF:

0.496

AC:

1721

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.1

(source)

DANN

Benign

0.36

PhyloP100

-0.32

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over