rs10074645

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047416828.1(PRELID2):​c.*11-69983G>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
XM_047416828.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.998
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
PRELID2XM_047416828.1 linkuse as main transcriptc.*11-69983G>A intron_variant XP_047272784.1
PRELID2XM_047416830.1 linkuse as main transcriptc.*11-112507G>A intron_variant XP_047272786.1
PRELID2XM_047416832.1 linkuse as main transcriptc.*43-69983G>A intron_variant XP_047272788.1
PRELID2XR_007058586.1 linkuse as main transcriptn.636-112507G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRELID2ENST00000510259.5 linkuse as main transcriptn.71-112507G>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27364
AN:
151858
Hom.:
4144
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.405
Gnomad4 AMR
AF:
0.231
Gnomad4 ASJ
AF:
0.0980
Gnomad4 EAS
AF:
0.125
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.0933
Gnomad4 NFE
AF:
0.0629
Gnomad4 OTH
AF:
0.143
Alfa
AF:
0.138
Hom.:
442
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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10074645; hg19: chr5-144965385; API