rs7448390

Variant names:

• chr5-144158939-T-C
• rs7448390
• NM_030799.9:c.*1458A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-144158939-T-C
• chr5-144158939-T-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.*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
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIPF5	NM_030799.9	MANE Select	c.*1458A>G		3_prime_UTR	Exon 6 of 6	NP_110426.4
	YIPF5	NM_001024947.4		c.*1458A>G		3_prime_UTR	Exon 6 of 6	NP_001020118.1
	YIPF5	NM_001271732.2		c.*1458A>G		3_prime_UTR	Exon 5 of 5	NP_001258661.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIPF5	ENST00000274496.10	TSL:1 MANE Select	c.*1458A>G		3_prime_UTR	Exon 6 of 6	ENSP00000274496.5
	YIPF5	ENST00000956131.1		c.*1458A>G		3_prime_UTR	Exon 6 of 6	ENSP00000626190.1

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

African (AFR) AF: 0.282 AC: 4417 AN: 15652

American (AMR) AF: 0.226 AC: 222 AN: 982

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 883 AN: 5128

East Asian (EAS) AF: 0.399 AC: 1445 AN: 3626

South Asian (SAS) AF: 0.247 AC: 4054 AN: 16382

European-Finnish (FIN) AF: 0.178 AC: 59 AN: 332

Middle Eastern (MID) AF: 0.210 AC: 340 AN: 1620

European-Non Finnish (NFE) AF: 0.199 AC: 151278 AN: 759652

Other (OTH) AF: 0.225 AC: 6113 AN: 27228

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

African (AFR) AF: 0.266 AC: 10938 AN: 41142

American (AMR) AF: 0.213 AC: 3234 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3464

East Asian (EAS) AF: 0.398 AC: 2044 AN: 5140

South Asian (SAS) AF: 0.261 AC: 1248 AN: 4784

European-Finnish (FIN) AF: 0.221 AC: 2252 AN: 10206

Middle Eastern (MID) AF: 0.224 AC: 65 AN: 290

European-Non Finnish (NFE) AF: 0.201 AC: 13604 AN: 67708

Other (OTH) AF: 0.231 AC: 486 AN: 2100

Alfa AF: 0.142 Hom.: 446

Bravo AF: 0.232

Asia WGS AF: 0.330 AC: 1133 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.44
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: rs7448390; hg19: chr5-143538503;