NM_030799.9:c.110+2031C>T

Variant names:

• chr5-144167815-G-A
• rs6887645
• NM_030799.9:c.110+2031C>T

Variant summary

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

The NM_030799.9(YIPF5):​c.110+2031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,144 control chromosomes in the GnomAD database, including 1,822 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 0.15 (1822 hom., cov: 32)
• Consequence: YIPF5 NM_030799.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIPF5	NM_030799.9	c.110+2031C>T		intron_variant	Intron 2 of 5	ENST00000274496.10	NP_110426.4
YIPF5	NM_001024947.4	c.110+2031C>T		intron_variant	Intron 2 of 5		NP_001020118.1
YIPF5	NM_001271732.2	c.-52-2211C>T		intron_variant	Intron 1 of 4		NP_001258661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIPF5	ENST00000274496.10	c.110+2031C>T		intron_variant	Intron 2 of 5	1	NM_030799.9	ENSP00000274496.5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22320 AN: 152026 Hom.: 1820 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.169

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22327 AN: 152144 Hom.: 1822 Cov.: 32 AF XY: 0.146 AC XY: 10879 AN XY: 74380

African (AFR) AF: 0.107 AC: 4424 AN: 41528

American (AMR) AF: 0.243 AC: 3709 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3470

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5184

South Asian (SAS) AF: 0.144 AC: 696 AN: 4818

European-Finnish (FIN) AF: 0.101 AC: 1067 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11129 AN: 67960

Other (OTH) AF: 0.167 AC: 353 AN: 2112

Alfa AF: 0.159 Hom.: 269

Bravo AF: 0.157

Asia WGS AF: 0.0840 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.62
PhyloP100		-0.067
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: rs6887645; hg19: chr5-143547379;