chrX-37694445-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_021083.4(XK):c.405G>A(p.Ala135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000411 in 1,193,557 control chromosomes in the GnomAD database, including 1 homozygotes. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 1 hom., 4 hem., cov: 23)
Exomes 𝑓: 0.000027 ( 0 hom. 8 hem. )
Consequence
XK
NM_021083.4 synonymous
NM_021083.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
Genes affected
XK (HGNC:12811): (X-linked Kx blood group antigen, Kell and VPS13A binding protein) This locus controls the synthesis of the Kell blood group 'precursor substance' (Kx). Mutations in this gene have been associated with McLeod syndrome, an X-linked, recessive disorder characterized by abnormalities in the neuromuscular and hematopoietic systems. The encoded protein has structural characteristics of prokaryotic and eukaryotic membrane transport proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant X-37694445-G-A is Benign according to our data. Variant chrX-37694445-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2892420.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.28 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XK | NM_021083.4 | c.405G>A | p.Ala135= | synonymous_variant | 2/3 | ENST00000378616.5 | |
XK | XM_011543978.4 | c.405G>A | p.Ala135= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XK | ENST00000378616.5 | c.405G>A | p.Ala135= | synonymous_variant | 2/3 | 1 | NM_021083.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000152 AC: 17AN: 112027Hom.: 0 Cov.: 23 AF XY: 0.0000877 AC XY: 3AN XY: 34189
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GnomAD3 exomes AF: 0.0000528 AC: 8AN: 151467Hom.: 0 AF XY: 0.0000430 AC XY: 2AN XY: 46475
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GnomAD4 exome AF: 0.0000268 AC: 29AN: 1081479Hom.: 0 Cov.: 31 AF XY: 0.0000228 AC XY: 8AN XY: 351637
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GnomAD4 genome ? AF: 0.000178 AC: 20AN: 112078Hom.: 1 Cov.: 23 AF XY: 0.000117 AC XY: 4AN XY: 34250
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at