Variant rs140392 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000461808.5(ENSG00000291044):n.211+4838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 152,180 control chromosomes in the GnomAD database, including 114 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 0.011 ( 114 hom., cov: 32)

Consequence

ENSG00000291044
ENST00000461808.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Variant links:

Genes affected

ENSG00000291044 (HGNC:):

ENSG00000291044 links:

BCRP2 (HGNC:1015): (BCR pseudogene 2)

BCRP2 links:

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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCRP2	NR_037566.1 link	n.211+4838G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000291044	ENST00000461808.5 link	n.211+4838G>A	intron_variant	2
ENSG00000291044	ENST00000686994.1 link	n.323+1819G>A	intron_variant
ENSG00000291044	ENST00000687229.1 link	n.222+4838G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0112

AC:

1705

AN:

152062

Hom.:

116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00308

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.00246

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00165

Gnomad OTH

AF:

0.00670

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

GnomAD4 genome

AF:

0.0112

AC:

1700

AN:

152180

Hom.:

114

Cov.:

AF XY:

0.0137

AC XY:

1022

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.00140

Gnomad4 AMR

AF:

0.00308

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.140

Gnomad4 SAS

AF:

0.147

Gnomad4 FIN

AF:

0.00246

Gnomad4 NFE

AF:

0.00165

Gnomad4 OTH

AF:

0.00711

Alfa

AF:

0.00701

Hom.:

Bravo

AF:

0.00759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

5.4

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