rs2074000
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001163941.2(ABCB5):c.784C>A(p.Gln262Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,613,588 control chromosomes in the GnomAD database, including 7,768 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 0.044 ( 838 hom., cov: 33)
Exomes 𝑓: 0.033 ( 6930 hom. )
Consequence
ABCB5
NM_001163941.2 missense
NM_001163941.2 missense
Scores
1
8
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.91
Genes affected
ABCB5 (HGNC:46): (ATP binding cassette subfamily B member 5) ABCB5 belongs to the ATP-binding cassette (ABC) transporter superfamily of integral membrane proteins. These proteins participate in ATP-dependent transmembrane transport of structurally diverse molecules ranging from small ions, sugars, and peptides to more complex organic molecules (Chen et al., 2005 [PubMed 15760339]).[supplied by OMIM, Mar 2008]
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 (MetaRNN=0.004671544).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB5 | NM_001163941.2 | c.784C>A | p.Gln262Lys | missense_variant | 8/28 | ENST00000404938.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB5 | ENST00000404938.7 | c.784C>A | p.Gln262Lys | missense_variant | 8/28 | 1 | NM_001163941.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0438 AC: 6665AN: 152112Hom.: 834 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
6665
AN:
152112
Hom.:
Cov.:
33
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: 0.0927 AC: 23032AN: 248356Hom.: 3588 AF XY: 0.0836 AC XY: 11286AN XY: 134958
GnomAD3 exomes
AF:
AC:
23032
AN:
248356
Hom.:
AF XY:
AC XY:
11286
AN XY:
134958
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: 0.0328 AC: 48003AN: 1461358Hom.: 6930 Cov.: 30 AF XY: 0.0332 AC XY: 24168AN XY: 726936
GnomAD4 exome
AF:
AC:
48003
AN:
1461358
Hom.:
Cov.:
30
AF XY:
AC XY:
24168
AN XY:
726936
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: 0.0439 AC: 6683AN: 152230Hom.: 838 Cov.: 33 AF XY: 0.0529 AC XY: 3935AN XY: 74420
GnomAD4 genome
?
AF:
AC:
6683
AN:
152230
Hom.:
Cov.:
33
AF XY:
AC XY:
3935
AN XY:
74420
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:
TwinsUK
AF:
AC:
7
ALSPAC
AF:
AC:
13
ESP6500AA
AF:
AC:
20
ESP6500EA
AF:
AC:
46
ExAC
?
AF:
AC:
10003
Asia WGS
AF:
AC:
824
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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