4-88105276-A-C

Variant names:

• chr4-88105276-A-C
• rs2725263
• NM_004827.3:c.1277+1908T>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004827.3(ABCG2):​c.1277+1908T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,044 control chromosomes in the GnomAD database, including 16,624 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.44 (16624 hom., cov: 32)
• Consequence: ABCG2 NM_004827.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0450
• Publications: 10 publications found

Genes affected

ABCG2 (HGNC:74): (ATP binding cassette subfamily G member 2 (JR blood group)) The membrane-associated protein encoded by this gene is included in the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the White subfamily. Alternatively referred to as a breast cancer resistance protein, this protein functions as a xenobiotic transporter which may play a major role in multi-drug resistance. It likely serves as a cellular defense mechanism in response to mitoxantrone and anthracycline exposure. Significant expression of this protein has been observed in the placenta, which may suggest a potential role for this molecule in placenta tissue. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 4-88105276-A-C is Benign according to our data. Variant chr4-88105276-A-C is described in ClinVar as Benign. ClinVar VariationId is 1267736.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004827.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCG2	NM_004827.3	MANE Select	c.1277+1908T>G		intron	N/A	NP_004818.2	Q9UNQ0-1
	ABCG2	NM_001348985.1		c.1277+1908T>G		intron	N/A	NP_001335914.1	Q9UNQ0-1
	ABCG2	NM_001348986.2		c.1277+1908T>G		intron	N/A	NP_001335915.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCG2	ENST00000237612.8	TSL:1 MANE Select	c.1277+1908T>G		intron	N/A	ENSP00000237612.3	Q9UNQ0-1
	ABCG2	ENST00000515655.5	TSL:1	c.1277+1908T>G		intron	N/A	ENSP00000426917.1	Q9UNQ0-2
	ABCG2	ENST00000889086.1		c.1364+1908T>G		intron	N/A	ENSP00000559145.1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66858 AN: 151926 Hom.: 16607 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.440 AC: 66909 AN: 152044 Hom.: 16624 Cov.: 32 AF XY: 0.435 AC XY: 32316 AN XY: 74304

African (AFR) AF: 0.194 AC: 8069 AN: 41510

American (AMR) AF: 0.497 AC: 7581 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2058 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2925 AN: 5174

South Asian (SAS) AF: 0.505 AC: 2432 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4325 AN: 10552

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.557 AC: 37872 AN: 67964

Other (OTH) AF: 0.486 AC: 1024 AN: 2108

Alfa AF: 0.509 Hom.: 43252

Bravo AF: 0.440

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		0.045
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2725263; hg19: chr4-89026428;