XM_017009130.2:c.*426G>A

Variant names:

• chr5-145664930-C-T
• rs17103583
• XM_017009130.2:c.*426G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_017009130.2(PRELID2):​c.*426G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,864 control chromosomes in the GnomAD database, including 5,916 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 0.21 (5916 hom., cov: 32)
• Consequence: PRELID2 XM_017009130.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 2 publications found

Genes affected

PRELID2 (HGNC:28306): (PRELI domain containing 2) Predicted to enable phosphatidic acid transfer activity. Predicted to be involved in phospholipid transport. Predicted to be active in mitochondrial intermembrane space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRELID2	XM_017009130.2	c.*426G>A		3_prime_UTR_variant	Exon 8 of 8		XP_016864619.1
PRELID2	XM_017009133.2	c.*458G>A		3_prime_UTR_variant	Exon 7 of 7		XP_016864622.1
PRELID2	XM_047416828.1	c.*10+100001G>A		intron_variant	Intron 7 of 7		XP_047272784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5	n.70+100001G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31281 AN: 151746 Hom.: 5891 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.206 AC: 31356 AN: 151864 Hom.: 5916 Cov.: 32 AF XY: 0.206 AC XY: 15303 AN XY: 74240

African (AFR) AF: 0.496 AC: 20541 AN: 41386

American (AMR) AF: 0.241 AC: 3663 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.145 AC: 746 AN: 5148

South Asian (SAS) AF: 0.110 AC: 532 AN: 4818

European-Finnish (FIN) AF: 0.0918 AC: 971 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4232 AN: 67952

Other (OTH) AF: 0.160 AC: 336 AN: 2102

Alfa AF: 0.122 Hom.: 509

Bravo AF: 0.233

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	19
DANN	Benign	0.57
PhyloP100		1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17103583; hg19: chr5-145044493;