XM_017009130.2:c.*6088A>G

Variant names:

• chr5-145659268-T-C
• rs10515552
• XM_017009130.2:c.*6088A>G

Variant summary

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

The XM_017009130.2(PRELID2):​c.*6088A>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 0.0686 in 152,256 control chromosomes in the GnomAD database, including 546 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 0.069 (546 hom., cov: 32)
• Consequence: PRELID2 XM_017009130.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 12 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510259.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID2	ENST00000510259.5	TSL:3	n.70+105663A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10430 AN: 152138 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0686 AC: 10440 AN: 152256 Hom.: 546 Cov.: 32 AF XY: 0.0732 AC XY: 5445 AN XY: 74432

African (AFR) AF: 0.0570 AC: 2368 AN: 41568

American (AMR) AF: 0.182 AC: 2776 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3470

East Asian (EAS) AF: 0.132 AC: 681 AN: 5162

South Asian (SAS) AF: 0.105 AC: 507 AN: 4828

European-Finnish (FIN) AF: 0.0768 AC: 813 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0443 AC: 3011 AN: 68024

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0518 Hom.: 1350

Bravo AF: 0.0768

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.72
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10515552; hg19: chr5-145038831;