rs1865009

chr5-145610070-T-Achr5-145610070-T-C

Variant summary

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

The XM_047416828.1(PRELID2):c.*11-94231A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,180 control chromosomes in the GnomAD database, including 2,236 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 0.14 (2236 hom., cov: 32)
• Consequence: PRELID2 XM_047416828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRELID2	XM_047416828.1	c.*11-94231A>T		intron_variant
PRELID2	XM_047416830.1	c.*11-136755A>T		intron_variant
PRELID2	XM_047416832.1	c.*43-94231A>T		intron_variant
PRELID2	XR_007058586.1	n.636-136755A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-136755A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21313 AN: 152062 Hom.: 2222 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.140 AC: 21362 AN: 152180 Hom.: 2236 Cov.: 32 AF XY: 0.142 AC XY: 10528 AN XY: 74396

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.106

Alfa AF: 0.113 Hom.: 203

Bravo AF: 0.156

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1865009; hg19: chr5-144989633;