chr5-144158939-T-C

Position:

• chr5-144158939-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030799.9(YIPF5):​c.*1458A>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 0.207 in 981,528 control chromosomes in the GnomAD database, including 21,788 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 0.23 (4130 hom., cov: 30)
  • Exomes 𝑓: 0.20 (17658 hom.)
• Consequence: YIPF5 NM_030799.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YIPF5	NM_030799.9	c.*1458A>G		3_prime_UTR_variant	6/6	ENST00000274496.10	NP_110426.4
YIPF5	NM_001024947.4	c.*1458A>G		3_prime_UTR_variant	6/6		NP_001020118.1
YIPF5	NM_001271732.2	c.*1458A>G		3_prime_UTR_variant	5/5		NP_001258661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YIPF5	ENST00000274496.10	c.*1458A>G		3_prime_UTR_variant	6/6	1	NM_030799.9	ENSP00000274496	P1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34645 AN: 150826 Hom.: 4125 Cov.: 30

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.203 AC: 168811 AN: 830602 Hom.: 17658 Cov.: 32 AF XY: 0.202 AC XY: 77587 AN XY: 383854

Gnomad4 AFR exome AF: 0.282

Gnomad4 AMR exome AF: 0.226

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.399

Gnomad4 SAS exome AF: 0.247

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.199

Gnomad4 OTH exome AF: 0.225

GnomAD4 genome AF: 0.230 AC: 34694 AN: 150926 Hom.: 4130 Cov.: 30 AF XY: 0.231 AC XY: 17005 AN XY: 73762

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.231

Alfa AF: 0.138 Hom.: 413

Bravo AF: 0.232

Asia WGS AF: 0.330 AC: 1133 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.65

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: rs7448390; hg19: chr5-143538503;