5-145526893-A-G

Position:

• chr5-145526893-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047416828.1(PRELID2):​c.*11-11054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,018 control chromosomes in the GnomAD database, including 21,552 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 0.52 (21552 hom., cov: 32)
• Consequence: PRELID2 XM_047416828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRELID2	XM_047416828.1	c.*11-11054T>C		intron_variant
PRELID2	XM_047416830.1	c.*11-53578T>C		intron_variant
PRELID2	XM_047416832.1	c.*43-11054T>C		intron_variant
PRELID2	XR_007058586.1	n.636-53578T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-53578T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79049 AN: 151900 Hom.: 21520 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.520 AC: 79122 AN: 152018 Hom.: 21552 Cov.: 32 AF XY: 0.529 AC XY: 39322 AN XY: 74284

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.523

Alfa AF: 0.465 Hom.: 22941

Bravo AF: 0.532

Asia WGS AF: 0.801 AC: 2780 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363556; hg19: chr5-144906456;