rs59334881
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001163941.2(ABCB5):c.3370G>A(p.Glu1124Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,614,178 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 29 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 34 hom. )
Consequence
ABCB5
NM_001163941.2 missense
NM_001163941.2 missense
Scores
2
8
7
Clinical Significance
Conservation
PhyloP100: 9.93
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008663893).
BP6
?
Variant 7-20745379-G-A is Benign according to our data. Variant chr7-20745379-G-A is described in ClinVar as [Benign]. Clinvar id is 785211.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1737/152304) while in subpopulation AFR AF= 0.0397 (1650/41564). AF 95% confidence interval is 0.0381. There are 29 homozygotes in gnomad4. There are 806 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB5 | NM_001163941.2 | c.3370G>A | p.Glu1124Lys | missense_variant | 26/28 | ENST00000404938.7 | |
ABCB5 | NM_178559.6 | c.2035G>A | p.Glu679Lys | missense_variant | 17/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB5 | ENST00000404938.7 | c.3370G>A | p.Glu1124Lys | missense_variant | 26/28 | 1 | NM_001163941.2 | P1 | |
ABCB5 | ENST00000258738.10 | c.2035G>A | p.Glu679Lys | missense_variant | 17/19 | 1 | |||
ABCB5 | ENST00000441315.1 | c.871G>A | p.Glu291Lys | missense_variant, NMD_transcript_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1737AN: 152186Hom.: 29 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1737
AN:
152186
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: 0.00297 AC: 747AN: 251456Hom.: 8 AF XY: 0.00207 AC XY: 281AN XY: 135896
GnomAD3 exomes
AF:
AC:
747
AN:
251456
Hom.:
AF XY:
AC XY:
281
AN XY:
135896
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: 0.00121 AC: 1776AN: 1461874Hom.: 34 Cov.: 31 AF XY: 0.00104 AC XY: 757AN XY: 727244
GnomAD4 exome
AF:
AC:
1776
AN:
1461874
Hom.:
Cov.:
31
AF XY:
AC XY:
757
AN XY:
727244
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: 0.0114 AC: 1737AN: 152304Hom.: 29 Cov.: 33 AF XY: 0.0108 AC XY: 806AN XY: 74478
GnomAD4 genome
?
AF:
AC:
1737
AN:
152304
Hom.:
Cov.:
33
AF XY:
AC XY:
806
AN XY:
74478
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:
ESP6500AA
AF:
AC:
148
ESP6500EA
AF:
AC:
2
ExAC
?
AF:
AC:
426
Asia WGS
AF:
AC:
6
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Benign
D;D
Sift4G
Uncertain
T;D
Vest4
MVP
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