22-21108064-G-A

Variant names:

• chr22-21108064-G-A
• rs140392
• ENST00000461808.5:n.211+4838G>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+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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461808.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCRP2	NR_037566.1		n.211+4838G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291044	ENST00000461808.5	TSL:2	n.211+4838G>A		intron	N/A
	ENSG00000291044	ENST00000686994.2		n.355+1819G>A		intron	N/A
	ENSG00000291044	ENST00000687229.2		n.222+4838G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 1705 AN: 152062 Hom.: 116 Cov.: 32

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.: 32 AF XY: 0.0137 AC XY: 1022 AN XY: 74392

African (AFR) AF: 0.00140 AC: 58 AN: 41524

American (AMR) AF: 0.00308 AC: 47 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.140 AC: 728 AN: 5186

South Asian (SAS) AF: 0.147 AC: 710 AN: 4814

European-Finnish (FIN) AF: 0.00246 AC: 26 AN: 10584

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00165 AC: 112 AN: 68006

Other (OTH) AF: 0.00711 AC: 15 AN: 2110

Alfa AF: 0.00560 Hom.: 74

Bravo AF: 0.00759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs140392; hg19: chr22-21462353;