5-145638921-C-T

Position:

• chr5-145638921-C-T

Variant summary

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

The XM_047416828.1(PRELID2):​c.*11-123082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,184 control chromosomes in the GnomAD database, including 7,178 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 0.22 (7178 hom., cov: 32)
• Consequence: PRELID2 XM_047416828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRELID2	XM_047416828.1	c.*11-123082G>A		intron_variant
PRELID2	XM_047416830.1	c.*10+126010G>A		intron_variant
PRELID2	XM_047416832.1	c.*43-123082G>A		intron_variant
PRELID2	XR_007058586.1	n.635+126010G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRELID2	ENST00000510259.5	n.70+126010G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33876 AN: 152066 Hom.: 7140 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.223 AC: 33972 AN: 152184 Hom.: 7178 Cov.: 32 AF XY: 0.222 AC XY: 16506 AN XY: 74402

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0910

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.175

Alfa AF: 0.128 Hom.: 601

Bravo AF: 0.252

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.063
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6893183; hg19: chr5-145018484;