rs7713855

Variant names:

• chr5-145544941-T-C
• rs7713855
• ENST00000510259.5:n.71-71626A>G

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-71626A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,058 control chromosomes in the GnomAD database, including 1,778 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 0.15 (1778 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 3 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=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRELID2	XM_047416828.1	c.*11-29102A>G		intron_variant	Intron 7 of 7		XP_047272784.1
PRELID2	XM_047416830.1	c.*11-71626A>G		intron_variant	Intron 6 of 6		XP_047272786.1
PRELID2	XM_047416832.1	c.*43-29102A>G		intron_variant	Intron 6 of 6		XP_047272788.1
PRELID2	XR_007058586.1	n.636-71626A>G		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5	n.71-71626A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22548 AN: 151940 Hom.: 1778 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.148 AC: 22557 AN: 152058 Hom.: 1778 Cov.: 32 AF XY: 0.146 AC XY: 10858 AN XY: 74338

African (AFR) AF: 0.0952 AC: 3953 AN: 41502

American (AMR) AF: 0.139 AC: 2124 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3464

East Asian (EAS) AF: 0.0694 AC: 358 AN: 5162

South Asian (SAS) AF: 0.155 AC: 748 AN: 4822

European-Finnish (FIN) AF: 0.184 AC: 1953 AN: 10588

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12218 AN: 67946

Other (OTH) AF: 0.142 AC: 300 AN: 2110

Alfa AF: 0.171 Hom.: 1299

Bravo AF: 0.143

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs7713855; hg19: chr5-144924504;