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GeneBe

rs1128503

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001348946.2(ABCB1):c.1236T>C(p.Gly412=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151856 control chromosomes in the gnomAD Genomes database, including 30269 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 30269 hom., cov: 32)
Exomes 𝑓: 0.54 ( 37666 hom. )

Consequence

ABCB1
NM_001348946.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2O:1

Conservation

PhyloP100: -0.153

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 7-87550285-A-G is Benign according to our data. Variant chr7-87550285-A-G is described in ClinVar as [Benign]. Clinvar id is 194187. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-87550285-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.153 with no splicing effect.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABCB1NM_001348946.2 linkuse as main transcriptc.1236T>C p.Gly412= synonymous_variant 12/28 ENST00000622132.5
ABCB1NM_001348945.2 linkuse as main transcriptc.1446T>C p.Gly482= synonymous_variant 16/32
ABCB1NM_000927.5 linkuse as main transcriptc.1236T>C p.Gly412= synonymous_variant 13/29
ABCB1NM_001348944.2 linkuse as main transcriptc.1236T>C p.Gly412= synonymous_variant 14/30

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCB1ENST00000622132.5 linkuse as main transcriptc.1236T>C p.Gly412= synonymous_variant 12/281 NM_001348946.2 P1P08183-1
ABCB1ENST00000265724.8 linkuse as main transcriptc.1236T>C p.Gly412= synonymous_variant 13/291 P1P08183-1
ABCB1ENST00000543898.5 linkuse as main transcriptc.1044T>C p.Gly348= synonymous_variant 12/285 P08183-2

Frequencies

GnomAD3 genomes
AF:
0.619
AC:
93943
AN:
151856
Hom.:
30269
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.806
Gnomad AMI
AF:
0.669
Gnomad AMR
AF:
0.573
Gnomad ASJ
AF:
0.634
Gnomad EAS
AF:
0.365
Gnomad SAS
AF:
0.400
Gnomad FIN
AF:
0.515
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.622
GnomAD3 exomes
AF:
0.537
AC:
134826
AN:
251258
Hom.:
37666
AF XY:
0.527
AC XY:
71570
AN XY:
135790
show subpopulations
Gnomad AFR exome
AF:
0.811
Gnomad AMR exome
AF:
0.511
Gnomad ASJ exome
AF:
0.633
Gnomad EAS exome
AF:
0.357
Gnomad SAS exome
AF:
0.393
Gnomad FIN exome
AF:
0.513
Gnomad NFE exome
AF:
0.568
Gnomad OTH exome
AF:
0.552
GnomAD4 exome
AF:
0.553
AC:
807661
AN:
1461784
Hom.:
226668
AF XY:
0.547
AC XY:
397991
AN XY:
727196
show subpopulations
Gnomad4 AFR exome
AF:
0.822
Gnomad4 AMR exome
AF:
0.514
Gnomad4 ASJ exome
AF:
0.643
Gnomad4 EAS exome
AF:
0.376
Gnomad4 SAS exome
AF:
0.395
Gnomad4 FIN exome
AF:
0.517
Gnomad4 NFE exome
AF:
0.564
Gnomad4 OTH exome
AF:
0.556
Alfa
AF:
0.577
Hom.:
54035
Bravo
AF:
0.632
Asia WGS
AF:
0.429
AC:
1498
AN:
3478
EpiCase
AF:
0.561
EpiControl
AF:
0.563

ClinVar

Significance: Benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Aug 06, 2014- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMar 13, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Tramadol response Other:1
drug response, no assertion criteria providedresearchBruce Budowle Laboratory, University of North Texas Health Science CenterApr 28, 2018- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
4.3
Dann
Benign
0.45

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: rs1128503; hg19: chr7-87179601; COSMIC: COSV55946864; COSMIC: COSV55946864; API