22-21109441-G-A

Variant names:

• chr22-21109441-G-A
• rs2845421
• ENST00000461808.5:n.211+6215G>A

Variant summary

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

The ENST00000461808.5(ENSG00000291044):​n.211+6215G>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 151,788 control chromosomes in the GnomAD database, including 3,322 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 (3322 hom., cov: 30)
• Consequence: ENSG00000291044 ENST00000461808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCRP2	NR_037566.1	n.211+6215G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291044	ENST00000461808.5	n.211+6215G>A		intron_variant	Intron 1 of 5	2
ENSG00000291044	ENST00000686994.2	n.355+3196G>A		intron_variant	Intron 2 of 5
ENSG00000291044	ENST00000687229.2	n.222+6215G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27459 AN: 151670 Hom.: 3317 Cov.: 30

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.181 AC: 27488 AN: 151788 Hom.: 3322 Cov.: 30 AF XY: 0.189 AC XY: 14000 AN XY: 74156

African (AFR) AF: 0.176 AC: 7291 AN: 41372

American (AMR) AF: 0.322 AC: 4896 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3124 AN: 5158

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4812

European-Finnish (FIN) AF: 0.176 AC: 1852 AN: 10546

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8300 AN: 67906

Other (OTH) AF: 0.189 AC: 398 AN: 2102

Alfa AF: 0.147 Hom.: 2677

Bravo AF: 0.196

Asia WGS AF: 0.412 AC: 1427 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.23
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs2845421; hg19: chr22-21463730;