chr4-88157772-T-C

Variant names:

• chr4-88157772-T-C
• rs2622604
• NM_004827.3:c.-20+614A>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.-20+614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,060 control chromosomes in the GnomAD database, including 48,752 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 0.80 (48752 hom., cov: 31)
• Consequence: ABCG2 NM_004827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 45 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCG2	NM_004827.3	c.-20+614A>G		intron_variant	Intron 1 of 15	ENST00000237612.8	NP_004818.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCG2	ENST00000237612.8	c.-20+614A>G		intron_variant	Intron 1 of 15	1	NM_004827.3	ENSP00000237612.3

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121351 AN: 151942 Hom.: 48703 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.799 AC: 121450 AN: 152060 Hom.: 48752 Cov.: 31 AF XY: 0.797 AC XY: 59241 AN XY: 74320

African (AFR) AF: 0.874 AC: 36258 AN: 41496

American (AMR) AF: 0.805 AC: 12287 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2961 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4199 AN: 5174

South Asian (SAS) AF: 0.847 AC: 4081 AN: 4816

European-Finnish (FIN) AF: 0.745 AC: 7853 AN: 10538

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51077 AN: 67980

Other (OTH) AF: 0.804 AC: 1701 AN: 2116

Alfa AF: 0.779 Hom.: 97408

Bravo AF: 0.807

Asia WGS AF: 0.828 AC: 2872 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.24
PhyloP100		-1.7
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: rs2622604; hg19: chr4-89078924;