rs3909378

Variant names:

• chr5-145457527-C-T
• rs3909378
• XR_001742911.2:n.60-21474C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001742911.2(LOC105378211):​n.60-21474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 152,204 control chromosomes in the GnomAD database, including 15 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 0.011 (15 hom., cov: 32)
• Consequence: LOC105378211 XR_001742911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

Genes affected

LOC105378211 (HGNC:):

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=-1.0).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0106 (1610/152204) while in subpopulation AFR AF = 0.0232 (964/41550). AF 95% confidence interval is 0.022. There are 15 homozygotes in GnomAd4. There are 767 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378211	XR_001742911.2	n.60-21474C>T		intron_variant	Intron 1 of 2
PRELID2	XR_007058586.1	n.751+15673G>A		intron_variant	Intron 7 of 9
LOC105378211	XR_007058983.1	n.60-21474C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0105 AC: 1593 AN: 152086 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.00623

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00665

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0106 AC: 1610 AN: 152204 Hom.: 15 Cov.: 32 AF XY: 0.0103 AC XY: 767 AN XY: 74398

African (AFR) AF: 0.0232 AC: 964 AN: 41550

American (AMR) AF: 0.00622 AC: 95 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4824

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10590

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00665 AC: 452 AN: 67998

Other (OTH) AF: 0.0104 AC: 22 AN: 2116

Alfa AF: 0.00881 Hom.: 0

Bravo AF: 0.0119

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.090
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3909378; hg19: chr5-144837090;