5-145526893-A-G

Variant names:

• chr5-145526893-A-G
• rs1363556
• XM_047416828.1:c.*11-11054T>C

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-53578T>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 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID2	ENST00000510259.5	TSL:3	n.71-53578T>C		intron	N/A

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

African (AFR) AF: 0.581 AC: 24109 AN: 41462

American (AMR) AF: 0.565 AC: 8628 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1734 AN: 3464

East Asian (EAS) AF: 0.921 AC: 4769 AN: 5178

South Asian (SAS) AF: 0.738 AC: 3556 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4746 AN: 10572

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29992 AN: 67952

Other (OTH) AF: 0.523 AC: 1105 AN: 2114

Alfa AF: 0.471 Hom.: 31696

Bravo AF: 0.532

Asia WGS AF: 0.801 AC: 2780 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.86
PhyloP100		-0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1363556;

hg19: chr5-144906456;