Variant 5-144165488-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_030799.9(YIPF5):c.227C>T(p.Ala76Val) variant causes a missense change. The variant allele was found at a frequency of 0.021 in 1,614,122 control chromosomes in the GnomAD database, including 413 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 26 hom., cov: 32)

Exomes 𝑓: 0.022 ( 387 hom. )

Consequence

YIPF5
NM_030799.9 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.80

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004816413).

BP6

Variant 5-144165488-G-A is Benign according to our data. Variant chr5-144165488-G-A is described in ClinVar as [Benign]. Clinvar id is 2655875.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0149 (2264/152276) while in subpopulation NFE AF= 0.0245 (1667/68014). AF 95% confidence interval is 0.0235. There are 26 homozygotes in gnomad4. There are 1000 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 26 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
YIPF5	NM_030799.9 linkuse as main transcript	c.227C>T	p.Ala76Val	missense_variant	3/6	ENST00000274496.10	NP_110426.4
YIPF5	NM_001024947.4 linkuse as main transcript	c.227C>T	p.Ala76Val	missense_variant	3/6		NP_001020118.1
YIPF5	NM_001271732.2 linkuse as main transcript	c.65C>T	p.Ala22Val	missense_variant	2/5		NP_001258661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YIPF5	ENST00000274496.10 linkuse as main transcript	c.227C>T	p.Ala76Val	missense_variant	3/6	1	NM_030799.9	ENSP00000274496	P1	Q969M3-1

Frequencies

GnomAD3 genomes

AF:

0.0149

AC:

2261

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00471

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0133

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00703

Gnomad FIN

AF:

0.00773

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0245

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.0141

AC:

3555

AN:

251470

Hom.:

AF XY:

0.0146

AC XY:

1981

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.00468

Gnomad AMR exome

AF:

0.00708

Gnomad ASJ exome

AF:

0.0119

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00657

Gnomad FIN exome

AF:

0.0103

Gnomad NFE exome

AF:

0.0228

Gnomad OTH exome

AF:

0.0163

GnomAD4 exome

AF:

0.0217

AC:

31662

AN:

1461846

Hom.:

387

Cov.:

AF XY:

0.0212

AC XY:

15431

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.00424

Gnomad4 AMR exome

AF:

0.00751

Gnomad4 ASJ exome

AF:

0.0117

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00634

Gnomad4 FIN exome

AF:

0.0100

Gnomad4 NFE exome

AF:

0.0257

Gnomad4 OTH exome

AF:

0.0168

GnomAD4 genome

AF:

0.0149

AC:

2264

AN:

152276

Hom.:

Cov.:

AF XY:

0.0134

AC XY:

1000

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00469

Gnomad4 AMR

AF:

0.0133

Gnomad4 ASJ

AF:

0.00979

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00725

Gnomad4 FIN

AF:

0.00773

Gnomad4 NFE

AF:

0.0245

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0221

Hom.:

Bravo

AF:

0.0146

TwinsUK

AF:

0.0329

AC:

122

ALSPAC

AF:

0.0296

AC:

114

ESP6500AA

AF:

0.00477

AC:

ESP6500EA

AF:

0.0228

AC:

196

ExAC

AF:

0.0136

AC:

1656

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0265

EpiControl

AF:

0.0232

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2024

YIPF5: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.017

T;T;.;T;.

Eigen

Benign

-0.32

Eigen_PC

Benign

-0.24

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.72

.;T;T;T;T

MetaRNN

Benign

0.0048

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

L;L;.;.;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.68

N;N;N;N;N

REVEL

Benign

0.031

Sift

Benign

0.39

T;T;T;T;T

Sift4G

Benign

0.31

T;T;T;T;.

Polyphen

0.0

B;B;.;.;.

Vest4

0.099

MPC

0.12

ClinPred

0.0084

GERP RS

3.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.049

gMVP

0.36

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over