5-144159025-G-C

Variant names:

• chr5-144159025-G-C
• rs17101607
• NM_030799.9:c.*1372C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 8 publications found

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030799.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIPF5	NM_030799.9	MANE Select	c.*1372C>G		3_prime_UTR	Exon 6 of 6	NP_110426.4
	YIPF5	NM_001024947.4		c.*1372C>G		3_prime_UTR	Exon 6 of 6	NP_001020118.1
	YIPF5	NM_001271732.2		c.*1372C>G		3_prime_UTR	Exon 5 of 5	NP_001258661.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIPF5	ENST00000274496.10	TSL:1 MANE Select	c.*1372C>G		3_prime_UTR	Exon 6 of 6	ENSP00000274496.5
	YIPF5	ENST00000956131.1		c.*1372C>G		3_prime_UTR	Exon 6 of 6	ENSP00000626190.1
	YIPF5	ENST00000448443.6	TSL:1	c.*1372C>G		downstream_gene	N/A	ENSP00000397704.2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27590 AN: 151674 Hom.: 2631 Cov.: 32

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.: 31 AF XY: 0.170 AC XY: 65288 AN XY: 383136

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: 45 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

GnomAD4 genome AF: 0.182 AC: 27622 AN: 151782 Hom.: 2634 Cov.: 32 AF XY: 0.185 AC XY: 13704 AN XY: 74158

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: 56 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11501 AN: 67892

Other (OTH) AF: 0.188 AC: 397 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.36
DANN	Benign	0.49
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17101607; hg19: chr5-143538589;