rs458628

Variant names:

• chr2-32290329-G-A
• rs458628
• NM_032312.4:c.80-154G>A

Variant summary

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

The NM_032312.4(YIPF4):​c.80-154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,034 control chromosomes in the GnomAD database, including 31,213 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 0.63 (31213 hom., cov: 33)
• Consequence: YIPF4 NM_032312.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 4 publications found

Genes affected

YIPF4 (HGNC:28145): (Yip1 domain family member 4) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIPF4	NM_032312.4	c.80-154G>A		intron_variant	Intron 1 of 5	ENST00000238831.9	NP_115688.1
YIPF4	XM_005264599.4	c.80-154G>A		intron_variant	Intron 1 of 5		XP_005264656.1
YIPF4	XM_024453173.2	c.80-154G>A		intron_variant	Intron 1 of 4		XP_024308941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIPF4	ENST00000238831.9	c.80-154G>A		intron_variant	Intron 1 of 5	1	NM_032312.4	ENSP00000238831.3
YIPF4	ENST00000437765.1	n.5-154G>A		intron_variant	Intron 1 of 4	5		ENSP00000394339.1
YIPF4	ENST00000495355.1	n.107-154G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96359 AN: 151916 Hom.: 31171 Cov.: 33

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.634 AC: 96453 AN: 152034 Hom.: 31213 Cov.: 33 AF XY: 0.632 AC XY: 46947 AN XY: 74306

African (AFR) AF: 0.712 AC: 29553 AN: 41488

American (AMR) AF: 0.637 AC: 9713 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1658 AN: 5178

South Asian (SAS) AF: 0.462 AC: 2228 AN: 4826

European-Finnish (FIN) AF: 0.652 AC: 6879 AN: 10548

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.621 AC: 42182 AN: 67960

Other (OTH) AF: 0.616 AC: 1301 AN: 2112

Alfa AF: 0.628 Hom.: 8959

Bravo AF: 0.641

Asia WGS AF: 0.403 AC: 1399 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.43
PhyloP100		0.0020
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: rs458628; hg19: chr2-32515398;