chr5-145503513-C-A

Variant names:

• chr5-145503513-C-A
• rs13179436
• XM_047416830.1:c.*11-30198G>T

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-30198G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,786 control chromosomes in the GnomAD database, including 2,740 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 0.18 (2740 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 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.71-30198G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27218 AN: 151668 Hom.: 2737 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.179 AC: 27224 AN: 151786 Hom.: 2740 Cov.: 32 AF XY: 0.183 AC XY: 13554 AN XY: 74200

African (AFR) AF: 0.0946 AC: 3902 AN: 41254

American (AMR) AF: 0.188 AC: 2868 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3468

East Asian (EAS) AF: 0.0954 AC: 492 AN: 5158

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4818

European-Finnish (FIN) AF: 0.206 AC: 2170 AN: 10534

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14336 AN: 67984

Other (OTH) AF: 0.189 AC: 399 AN: 2114

Alfa AF: 0.195 Hom.: 3066

Bravo AF: 0.169

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.47
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs13179436; hg19: chr5-144883076;