Genetic Variant NM_030799.9:c.*1372C>G (chr5-144159025-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_030799.9(YIPF5):c.*1372C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 981,234 control chromosomes in the GnomAD database, including 15,053 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 0.18 ( 2634 hom., cov: 32)

Exomes 𝑓: 0.17 ( 12419 hom. )

Consequence

YIPF5
NM_030799.9 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

8 publications found

Variant links:

Genes affected

YIPF5 (HGNC:24877): (Yip1 domain family member 5) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; regulation of ER to Golgi vesicle-mediated transport; and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

YIPF5 Gene-Disease associations (from GenCC):

microcephaly, epilepsy, and diabetes syndrome 2
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
primary microcephaly-epilepsy-permanent neonatal diabetes syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

YIPF5 links:

Genome browser will be placed here

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
YIPF5	NM_030799.9 link	c.*1372C>G	3_prime_UTR_variant	Exon 6 of 6	ENST00000274496.10	NP_110426.4	Q969M3-1
YIPF5	NM_001024947.4 link	c.*1372C>G	3_prime_UTR_variant	Exon 6 of 6		NP_001020118.1	Q969M3-1
YIPF5	NM_001271732.2 link	c.*1372C>G	3_prime_UTR_variant	Exon 5 of 5		NP_001258661.1	Q969M3-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
YIPF5	ENST00000274496.10 link	c.*1372C>G	3_prime_UTR_variant	Exon 6 of 6	1	NM_030799.9	ENSP00000274496.5	Q969M3-1
YIPF5	ENST00000448443.6 link	c.*1372C>G	downstream_gene_variant		1		ENSP00000397704.2	Q969M3-1
YIPF5	ENST00000513112.5 link	c.*1372C>G	downstream_gene_variant		1		ENSP00000425422.1	Q969M3-2

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27590

AN:

151674

Hom.:

2631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.183

GnomAD4 exome

AF:

0.171

AC:

141887

AN:

829452

Hom.:

12419

Cov.:

AF XY:

0.170

AC XY:

65288

AN XY:

383136

show subpopulations

African (AFR)

AF:

0.175

AC:

2746

AN:

15676

American (AMR)

AF:

0.205

AC:

200

AN:

976

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

780

AN:

5134

East Asian (EAS)

AF:

0.361

AC:

1296

AN:

3594

South Asian (SAS)

AF:

0.204

AC:

3340

AN:

16382

European-Finnish (FIN)

AF:

0.164

AC:

AN:

274

Middle Eastern (MID)

AF:

0.174

AC:

280

AN:

1608

European-Non Finnish (NFE)

AF:

0.169

AC:

128106

AN:

758664

Other (OTH)

AF:

0.188

AC:

5094

AN:

27144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

5863

11726

17588

23451

29314

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6246

12492

18738

24984

31230

<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:

0.182

AC:

27622

AN:

151782

Hom.:

2634

Cov.:

AF XY:

0.185

AC XY:

13704

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.173

AC:

7160

AN:

41404

American (AMR)

AF:

0.177

AC:

2701

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

546

AN:

3460

East Asian (EAS)

AF:

0.358

AC:

1847

AN:

5156

South Asian (SAS)

AF:

0.216

AC:

1038

AN:

4810

European-Finnish (FIN)

AF:

0.212

AC:

2222

AN:

10498

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11501

AN:

67892

Other (OTH)

AF:

0.188

AC:

397

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1139

2279

3418

4558

5697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.158

Hom.:

244

Bravo

AF:

0.180

Asia WGS

AF:

0.288

AC:

996

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.36

(source)

DANN

Benign

0.49

PhyloP100

-0.097

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over