chr5-145610070-T-A

Variant names:

• chr5-145610070-T-A
• rs1865009
• XM_047416828.1:c.*11-94231A>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.

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.71-136755A>T		intron	N/A

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 v4.9

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;