rs13120400

Variant names:

• chr4-88112375-T-C
• rs13120400
• NM_004827.3:c.1194+928A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-88112375-T-C
• chr4-88112375-T-G

Variant summary

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

The NM_004827.3(ABCG2):​c.1194+928A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,026 control chromosomes in the GnomAD database, including 4,142 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 0.20 (4142 hom., cov: 31)
• Consequence: ABCG2 NM_004827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 44 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCG2	NM_004827.3	c.1194+928A>G		intron_variant	Intron 9 of 15	ENST00000237612.8	NP_004818.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCG2	ENST00000237612.8	c.1194+928A>G		intron_variant	Intron 9 of 15	1	NM_004827.3	ENSP00000237612.3
ABCG2	ENST00000515655.5	c.1194+928A>G		intron_variant	Intron 9 of 15	1		ENSP00000426917.1
ABCG2	ENST00000650821.1	c.1194+928A>G		intron_variant	Intron 10 of 16			ENSP00000498246.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30971 AN: 151906 Hom.: 4140 Cov.: 31

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.204 AC: 30967 AN: 152026 Hom.: 4142 Cov.: 31 AF XY: 0.205 AC XY: 15215 AN XY: 74318

African (AFR) AF: 0.0640 AC: 2657 AN: 41512

American (AMR) AF: 0.192 AC: 2930 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3466

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.112 AC: 539 AN: 4822

European-Finnish (FIN) AF: 0.344 AC: 3620 AN: 10534

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19998 AN: 67914

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.240 Hom.: 10258

Bravo AF: 0.185

Asia WGS AF: 0.0590 AC: 207 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	0.19
DANN	Benign	0.76
PhyloP100		-3.0
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: rs13120400; hg19: chr4-89033527;