rs1363554

chr5-145574361-G-A

Variant summary

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

The XM_047416828.1(PRELID2):c.*11-58522C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,158 control chromosomes in the GnomAD database, including 2,365 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 0.11 (2365 hom., cov: 32)
• Consequence: PRELID2 XM_047416828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRELID2	XM_047416828.1	c.*11-58522C>T		intron_variant
PRELID2	XM_047416830.1	c.*11-101046C>T		intron_variant
PRELID2	XM_047416832.1	c.*43-58522C>T		intron_variant
PRELID2	XR_007058586.1	n.636-101046C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-101046C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16224 AN: 152040 Hom.: 2349 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0465

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.107 AC: 16280 AN: 152158 Hom.: 2365 Cov.: 32 AF XY: 0.103 AC XY: 7635 AN XY: 74402

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.0464

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.00415

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0697 Hom.: 147

Bravo AF: 0.119

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363554; hg19: chr5-144953924;