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GeneBe

rs2231142

chr4-88131171-G-Achr4-88131171-G-Cchr4-88131171-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2_SupportingPM4

The NM_004827.3(ABCG2):c.421C>T(p.Gln141Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

ABCG2
NM_004827.3 stop_gained

Scores

4
2
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
PM4
?
Stoplost variant in NM_004827.3 Downstream stopcodon found after 44 codons.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABCG2NM_004827.3 linkuse as main transcriptc.421C>T p.Gln141Ter stop_gained 5/16 ENST00000237612.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCG2ENST00000237612.8 linkuse as main transcriptc.421C>T p.Gln141Ter stop_gained 5/161 NM_004827.3 P1Q9UNQ0-1
ABCG2ENST00000515655.5 linkuse as main transcriptc.421C>T p.Gln141Ter stop_gained 5/161 Q9UNQ0-2
ABCG2ENST00000650821.1 linkuse as main transcriptc.421C>T p.Gln141Ter stop_gained 6/17 P1Q9UNQ0-1

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.60
D
BayesDel_noAF
Pathogenic
0.62
Cadd
Pathogenic
37
Dann
Uncertain
1.0
Eigen
Pathogenic
0.95
Eigen_PC
Pathogenic
0.81
FATHMM_MKL
Uncertain
0.87
D
MutationTaster
Benign
1.0
A;A
Vest4
0.95
GERP RS
5.4

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-89052323;