5-144160405-C-T

Variant names:

• chr5-144160405-C-T
• rs147304369
• NM_030799.9:c.766G>A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM1 BP4_Strong BP6_Moderate BS2

The NM_030799.9(YIPF5):​c.766G>A​(p.Val256Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 1,611,456 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0059 (6 hom., cov: 32)
  • Exomes 𝑓: 0.0093 (92 hom.)
• Consequence: YIPF5 NM_030799.9 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.03

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PM1: In a chain Protein YIPF5 (size 256) in uniprot entity YIPF5_HUMAN there are 6 pathogenic changes around while only 1 benign (86%) in NM_030799.9
• BP4: Computational evidence support a benign effect (MetaRNN=0.0073158443).
• BP6: Variant 5-144160405-C-T is Benign according to our data. Variant chr5-144160405-C-T is described in ClinVar as [Benign]. Clinvar id is 2655874.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIPF5	NM_030799.9	c.766G>A	p.Val256Ile	missense_variant	Exon 6 of 6	ENST00000274496.10	NP_110426.4
YIPF5	NM_001024947.4	c.766G>A	p.Val256Ile	missense_variant	Exon 6 of 6		NP_001020118.1
YIPF5	NM_001271732.2	c.604G>A	p.Val202Ile	missense_variant	Exon 5 of 5		NP_001258661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIPF5	ENST00000274496.10	c.766G>A	p.Val256Ile	missense_variant	Exon 6 of 6	1	NM_030799.9	ENSP00000274496.5
YIPF5	ENST00000448443.6	c.766G>A	p.Val256Ile	missense_variant	Exon 6 of 6	1		ENSP00000397704.2
YIPF5	ENST00000513112.5	c.604G>A	p.Val202Ile	missense_variant	Exon 5 of 5	1		ENSP00000425422.1
YIPF5	ENST00000519064.5	c.*73G>A		downstream_gene_variant		2		ENSP00000429777.1

Frequencies

GnomAD3 genomes AF: 0.00592 AC: 900 AN: 152102 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00563

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0100

Gnomad OTH AF: 0.00480

GnomAD3 exomes AF: 0.00588 AC: 1472 AN: 250324 Hom.: 10 AF XY: 0.00602 AC XY: 815 AN XY: 135324

Gnomad AFR exome AF: 0.00154

Gnomad AMR exome AF: 0.00312

Gnomad ASJ exome AF: 0.00868

Gnomad EAS exome AF: 0.0000545

Gnomad SAS exome AF: 0.00145

Gnomad FIN exome AF: 0.000878

Gnomad NFE exome AF: 0.0101

Gnomad OTH exome AF: 0.00786

GnomAD4 exome AF: 0.00928 AC: 13543 AN: 1459236 Hom.: 92 Cov.: 31 AF XY: 0.00912 AC XY: 6618 AN XY: 725680

Gnomad4 AFR exome AF: 0.00144

Gnomad4 AMR exome AF: 0.00330

Gnomad4 ASJ exome AF: 0.00840

Gnomad4 EAS exome AF: 0.000126

Gnomad4 SAS exome AF: 0.00176

Gnomad4 FIN exome AF: 0.00146

Gnomad4 NFE exome AF: 0.0111

Gnomad4 OTH exome AF: 0.00854

GnomAD4 genome AF: 0.00591 AC: 900 AN: 152220 Hom.: 6 Cov.: 32 AF XY: 0.00564 AC XY: 420 AN XY: 74430

Gnomad4 AFR AF: 0.00164

Gnomad4 AMR AF: 0.00562

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00208

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.0100

Gnomad4 OTH AF: 0.00475

Alfa AF: 0.00871 Hom.: 12

Bravo AF: 0.00597

TwinsUK AF: 0.0116 AC: 43

ALSPAC AF: 0.0114 AC: 44

ESP6500AA AF: 0.000908 AC: 4

ESP6500EA AF: 0.0113 AC: 97

ExAC AF: 0.00587 AC: 713

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

YIPF5: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.64	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.66
DEOGEN2	Benign	0.0050	T;T;.
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.67
FATHMM_MKL	Benign	0.60	D
LIST_S2	Benign	0.80	.;T;T
MetaRNN	Benign	0.0073	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;N;.
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.17	N;N;N
REVEL	Benign	0.076
Sift	Benign	0.73	T;T;T
Sift4G	Benign	0.65	T;T;T
Polyphen		0.51	P;P;.
Vest4		0.070
MVP		0.043
MPC		0.094
ClinPred		0.0049	T
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.014
gMVP		0.43

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: rs147304369; hg19: chr5-143539969;