5-145610070-T-A

Variant names:

• chr5-145610070-T-A
• rs1865009
• ENST00000510259.5:n.71-136755A>T

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-136755A>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 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• 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=-0.92).
• 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 rank	MANE	Protein	UniProt
PRELID2	XM_047416828.1	c.*11-94231A>T		intron_variant	Intron 7 of 7		XP_047272784.1
PRELID2	XM_047416830.1	c.*11-136755A>T		intron_variant	Intron 6 of 6		XP_047272786.1
PRELID2	XM_047416832.1	c.*43-94231A>T		intron_variant	Intron 6 of 6		XP_047272788.1
PRELID2	XR_007058586.1	n.636-136755A>T		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-136755A>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.271 AC: 11237 AN: 41530

American (AMR) AF: 0.212 AC: 3235 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3470

East Asian (EAS) AF: 0.126 AC: 650 AN: 5152

South Asian (SAS) AF: 0.109 AC: 524 AN: 4816

European-Finnish (FIN) AF: 0.0929 AC: 986 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4217 AN: 68000

Other (OTH) AF: 0.106 AC: 223 AN: 2110

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1865009; hg19: chr5-144989633;