rs7699188

Variant names:

• chr4-88174909-G-A
• rs7699188
• ENST00000515655.5:c.-19-34895C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-88174909-G-A
• chr4-88174909-G-C

Variant summary

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

The ENST00000515655.5(ABCG2):​c.-19-34895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,010 control chromosomes in the GnomAD database, including 5,668 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 0.24 (5668 hom., cov: 32)
• Consequence: ABCG2 ENST00000515655.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 36 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCG2	NM_001348985.1	c.-19-34895C>T		intron_variant	Intron 2 of 16		NP_001335914.1
ABCG2	NM_001257386.2	c.-19-34895C>T		intron_variant	Intron 1 of 15		NP_001244315.1
ABCG2	XM_011532420.4	c.-19-34895C>T		intron_variant	Intron 3 of 17		XP_011530722.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCG2	ENST00000515655.5	c.-19-34895C>T		intron_variant	Intron 1 of 15	1		ENSP00000426917.1
ABCG2	ENST00000650821.1	c.-19-34895C>T		intron_variant	Intron 2 of 16			ENSP00000498246.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36070 AN: 151892 Hom.: 5657 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.237 AC: 36097 AN: 152010 Hom.: 5668 Cov.: 32 AF XY: 0.233 AC XY: 17310 AN XY: 74312

African (AFR) AF: 0.448 AC: 18531 AN: 41404

American (AMR) AF: 0.154 AC: 2356 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3472

East Asian (EAS) AF: 0.0777 AC: 403 AN: 5184

South Asian (SAS) AF: 0.198 AC: 952 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1433 AN: 10568

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10934 AN: 67978

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.0999 Hom.: 170

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.9
DANN	Benign	0.78
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7699188; hg19: chr4-89096061;