Variant rs7736046 details in Genebe, Genetics Data Aggregator

Variant summary

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

The XM_047416828.1(PRELID2):c.*11-76208G>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
XM_047416828.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

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]

PRELID2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	Effect	Protein
PRELID2	XM_047416828.1 linkuse as main transcript	c.*11-76208G>T	intron_variant	XP_047272784.1
PRELID2	XM_047416830.1 linkuse as main transcript	c.*11-118732G>T	intron_variant	XP_047272786.1
PRELID2	XM_047416832.1 linkuse as main transcript	c.*43-76208G>T	intron_variant	XP_047272788.1
PRELID2	XR_007058586.1 linkuse as main transcript	n.636-118732G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRELID2	ENST00000510259.5 linkuse as main transcript	n.71-118732G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.700

AC:

106292

AN:

151952

Hom.:

38872

Cov.:

show subpopulations

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.:

AF XY:

0.697

AC XY:

51781

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.924

Gnomad4 AMR

AF:

0.740

Gnomad4 ASJ

AF:

0.607

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.559

Gnomad4 FIN

AF:

0.566

Gnomad4 NFE

AF:

0.598

Gnomad4 OTH

AF:

0.688

Alfa

AF:

0.657

Hom.:

9544

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over