rs10074645

Variant names:

• chr5-145585822-C-T
• rs10074645
• ENST00000510259.5:n.71-112507G>A

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-112507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,976 control chromosomes in the GnomAD database, including 4,169 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 (4169 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRELID2	XM_047416828.1	c.*11-69983G>A		intron_variant	Intron 7 of 7		XP_047272784.1
PRELID2	XM_047416830.1	c.*11-112507G>A		intron_variant	Intron 6 of 6		XP_047272786.1
PRELID2	XM_047416832.1	c.*43-69983G>A		intron_variant	Intron 6 of 6		XP_047272788.1
PRELID2	XR_007058586.1	n.636-112507G>A		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-112507G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27364 AN: 151858 Hom.: 4144 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0933

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.181 AC: 27438 AN: 151976 Hom.: 4169 Cov.: 32 AF XY: 0.180 AC XY: 13394 AN XY: 74296

African (AFR) AF: 0.405 AC: 16805 AN: 41454

American (AMR) AF: 0.231 AC: 3521 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.125 AC: 645 AN: 5144

South Asian (SAS) AF: 0.109 AC: 525 AN: 4812

European-Finnish (FIN) AF: 0.0933 AC: 990 AN: 10606

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4272 AN: 67942

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.147 Hom.: 510

Bravo AF: 0.202

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.36
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10074645; hg19: chr5-144965385;