rs7736046

Variant names:

• chr5-145592047-C-A
• rs7736046
• ENST00000510259.5:n.71-118732G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-145592047-C-A
• chr5-145592047-C-G
• chr5-145592047-C-T

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-118732G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,070 control chromosomes in the GnomAD database, including 38,932 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 0.70 (38932 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRELID2	XM_047416828.1	c.*11-76208G>T		intron_variant	Intron 7 of 7		XP_047272784.1
PRELID2	XM_047416830.1	c.*11-118732G>T		intron_variant	Intron 6 of 6		XP_047272786.1
PRELID2	XM_047416832.1	c.*43-76208G>T		intron_variant	Intron 6 of 6		XP_047272788.1
PRELID2	XR_007058586.1	n.636-118732G>T		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-118732G>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106292 AN: 151952 Hom.: 38872 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.700 AC: 106412 AN: 152070 Hom.: 38932 Cov.: 32 AF XY: 0.697 AC XY: 51781 AN XY: 74310

African (AFR) AF: 0.924 AC: 38377 AN: 41522

American (AMR) AF: 0.740 AC: 11295 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2103 AN: 3466

East Asian (EAS) AF: 0.613 AC: 3157 AN: 5154

South Asian (SAS) AF: 0.559 AC: 2699 AN: 4824

European-Finnish (FIN) AF: 0.566 AC: 5961 AN: 10534

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40679 AN: 67978

Other (OTH) AF: 0.688 AC: 1456 AN: 2116

Alfa AF: 0.655 Hom.: 14949

Bravo AF: 0.725

Asia WGS AF: 0.630 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7736046; hg19: chr5-144971610;