rs1016752
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000334444.11(ABCC5):c.3414+50C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 1,508,722 control chromosomes in the GnomAD database, including 317,560 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 0.71 ( 40056 hom., cov: 30)
Exomes 𝑓: 0.63 ( 277504 hom. )
Consequence
ABCC5
ENST00000334444.11 intron
ENST00000334444.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.92
Genes affected
ABCC5 (HGNC:56): (ATP binding cassette subfamily C member 5) The protein encoded by this gene is a member of 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 MRP subfamily which is involved in multi-drug resistance. This protein functions in the cellular export of its substrate, cyclic nucleotides. This export contributes to the degradation of phosphodiesterases and possibly an elimination pathway for cyclic nucleotides. Studies show that this protein provides resistance to thiopurine anticancer drugs, 6-mercatopurine and thioguanine, and the anti-HIV drug 9-(2-phosphonylmethoxyethyl)adenine. This protein may be involved in resistance to thiopurines in acute lymphoblastic leukemia and antiretroviral nucleoside analogs in HIV-infected patients. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC5 | NM_005688.4 | c.3414+50C>G | intron_variant | ENST00000334444.11 | NP_005679.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC5 | ENST00000334444.11 | c.3414+50C>G | intron_variant | 1 | NM_005688.4 | ENSP00000333926 | P1 | |||
ABCC5 | ENST00000265586.10 | c.3285+50C>G | intron_variant | 5 | ENSP00000265586 | |||||
ABCC5 | ENST00000437205.5 | c.*2107+50C>G | intron_variant, NMD_transcript_variant | 5 | ENSP00000403510 |
Frequencies
GnomAD3 genomes AF: 0.714 AC: 108293AN: 151638Hom.: 40001 Cov.: 30
GnomAD3 genomes
AF:
AC:
108293
AN:
151638
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.669 AC: 113269AN: 169422Hom.: 38851 AF XY: 0.657 AC XY: 59906AN XY: 91178
GnomAD3 exomes
AF:
AC:
113269
AN:
169422
Hom.:
AF XY:
AC XY:
59906
AN XY:
91178
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.635 AC: 861524AN: 1356966Hom.: 277504 Cov.: 25 AF XY: 0.633 AC XY: 420696AN XY: 664572
GnomAD4 exome
AF:
AC:
861524
AN:
1356966
Hom.:
Cov.:
25
AF XY:
AC XY:
420696
AN XY:
664572
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.714 AC: 108407AN: 151756Hom.: 40056 Cov.: 30 AF XY: 0.708 AC XY: 52464AN XY: 74130
GnomAD4 genome
AF:
AC:
108407
AN:
151756
Hom.:
Cov.:
30
AF XY:
AC XY:
52464
AN XY:
74130
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2727
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at