rs1363554

Variant names:

• chr5-145574361-G-A
• rs1363554
• XM_047416828.1:c.*11-58522C>T

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-101046C>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 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 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.71-101046C>T		intron	N/A

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

African (AFR) AF: 0.330 AC: 13673 AN: 41462

American (AMR) AF: 0.0464 AC: 709 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3468

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5178

South Asian (SAS) AF: 0.00415 AC: 20 AN: 4824

European-Finnish (FIN) AF: 0.0157 AC: 167 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0186 AC: 1264 AN: 68016

Other (OTH) AF: 0.0795 AC: 168 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.76
PhyloP100		-0.78

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: rs1363554;

hg19: chr5-144953924;