22-21105719-A-G

Variant names:

• chr22-21105719-A-G
• rs140390
• ENST00000461808.5:n.211+2493A>G

Variant summary

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

The ENST00000461808.5(ENSG00000291044):​n.211+2493A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,092 control chromosomes in the GnomAD database, including 51,782 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 0.82 (51782 hom., cov: 30)
• Consequence: ENSG00000291044 ENST00000461808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 6 publications found

Genes affected

ENSG00000291044 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCRP2	NR_037566.1	n.211+2493A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291044	ENST00000461808.5	n.211+2493A>G		intron_variant	Intron 1 of 5	2
ENSG00000291044	ENST00000686994.2	n.244-415A>G		intron_variant	Intron 1 of 5
ENSG00000291044	ENST00000687229.2	n.222+2493A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125166 AN: 151974 Hom.: 51741 Cov.: 30

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.824 AC: 125262 AN: 152092 Hom.: 51782 Cov.: 30 AF XY: 0.823 AC XY: 61190 AN XY: 74344

African (AFR) AF: 0.880 AC: 36504 AN: 41490

American (AMR) AF: 0.866 AC: 13222 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2666 AN: 3470

East Asian (EAS) AF: 0.769 AC: 3984 AN: 5184

South Asian (SAS) AF: 0.612 AC: 2950 AN: 4820

European-Finnish (FIN) AF: 0.835 AC: 8816 AN: 10562

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54568 AN: 67982

Other (OTH) AF: 0.836 AC: 1766 AN: 2112

Alfa AF: 0.808 Hom.: 101662

Bravo AF: 0.834

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.77
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs140390; hg19: chr22-21460008;