rs1189428

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005845.5(ABCC4):​c.2456-11764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,804 control chromosomes in the GnomAD database, including 20,490 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 0.51 ( 20490 hom., cov: 31)

Consequence

ABCC4
NM_005845.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.258
Variant links:
Genes affected
ABCC4 (HGNC:55): (ATP binding cassette subfamily C member 4 (PEL blood group)) 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 family member plays a role in cellular detoxification as a pump for its substrate, organic anions. It may also function in prostaglandin-mediated cAMP signaling in ciliogenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]

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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ABCC4NM_005845.5 linkuse as main transcriptc.2456-11764A>G intron_variant ENST00000645237.2 NP_005836.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ABCC4ENST00000645237.2 linkuse as main transcriptc.2456-11764A>G intron_variant NM_005845.5 ENSP00000494609 P1O15439-1

Frequencies

GnomAD3 genomes
AF:
0.513
AC:
77790
AN:
151688
Hom.:
20480
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.404
Gnomad AMI
AF:
0.437
Gnomad AMR
AF:
0.580
Gnomad ASJ
AF:
0.440
Gnomad EAS
AF:
0.512
Gnomad SAS
AF:
0.701
Gnomad FIN
AF:
0.634
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.537
Gnomad OTH
AF:
0.509
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.513
AC:
77833
AN:
151804
Hom.:
20490
Cov.:
31
AF XY:
0.523
AC XY:
38767
AN XY:
74176
show subpopulations
Gnomad4 AFR
AF:
0.404
Gnomad4 AMR
AF:
0.581
Gnomad4 ASJ
AF:
0.440
Gnomad4 EAS
AF:
0.513
Gnomad4 SAS
AF:
0.700
Gnomad4 FIN
AF:
0.634
Gnomad4 NFE
AF:
0.537
Gnomad4 OTH
AF:
0.506
Alfa
AF:
0.546
Hom.:
11565
Bravo
AF:
0.499
Asia WGS
AF:
0.587
AC:
2044
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
0.90
DANN
Benign
0.49

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1189428; hg19: chr13-95780019; API