5-145592047-C-A

Variant names:

• chr5-145592047-C-A
• rs7736046
• XM_047416828.1:c.*11-76208G>T

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-118732G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,070 control chromosomes in the GnomAD database, including 38,932 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 0.70 (38932 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.917 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.71-118732G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106292 AN: 151952 Hom.: 38872 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.700 AC: 106412 AN: 152070 Hom.: 38932 Cov.: 32 AF XY: 0.697 AC XY: 51781 AN XY: 74310

African (AFR) AF: 0.924 AC: 38377 AN: 41522

American (AMR) AF: 0.740 AC: 11295 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2103 AN: 3466

East Asian (EAS) AF: 0.613 AC: 3157 AN: 5154

South Asian (SAS) AF: 0.559 AC: 2699 AN: 4824

European-Finnish (FIN) AF: 0.566 AC: 5961 AN: 10534

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40679 AN: 67978

Other (OTH) AF: 0.688 AC: 1456 AN: 2116

Alfa AF: 0.655 Hom.: 14949

Bravo AF: 0.725

Asia WGS AF: 0.630 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-0.17

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: rs7736046;

hg19: chr5-144971610;