rs13179436

Positions:

• chr5-145503513-C-A
• chr5-145503513-C-G

Variant summary

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

The XM_047416830.1(PRELID2):​c.*11-30198G>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 XM_047416830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRELID2	XM_047416830.1	c.*11-30198G>T		intron_variant			XP_047272786.1
PRELID2	XR_007058586.1	n.636-30198G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-30198G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.189

Alfa AF: 0.196 Hom.: 2497

Bravo AF: 0.169

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13179436; hg19: chr5-144883076;