5-145659268-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRELID2	XM_017009130.2	c.*6088A>G		3_prime_UTR_variant	Exon 8 of 8		XP_016864619.1
PRELID2	XM_017009133.2	c.*6120A>G		3_prime_UTR_variant	Exon 7 of 7		XP_016864622.1
PRELID2	XM_047416828.1	c.*10+105663A>G		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+105663A>G		intron_variant	Intron 1 of 2	3

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 v4.3

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;