chrX-37694337-T-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_021083.4(XK):c.297T>A(p.Pro99Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,097,724 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 0.0000055 ( 0 hom. 3 hem. )
Consequence
XK
NM_021083.4 synonymous
NM_021083.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.379
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=-0.5).
BP6
Variant X-37694337-T-A is Benign according to our data. Variant chrX-37694337-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 3012050.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.379 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XK | NM_021083.4 | c.297T>A | p.Pro99Pro | synonymous_variant | 2/3 | ENST00000378616.5 | NP_066569.1 | |
XK | XM_011543978.4 | c.297T>A | p.Pro99Pro | synonymous_variant | 2/3 | XP_011542280.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XK | ENST00000378616.5 | c.297T>A | p.Pro99Pro | synonymous_variant | 2/3 | 1 | NM_021083.4 | ENSP00000367879.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.171+268337T>A | intron_variant | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 genomes
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24
GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181969Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66511
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GnomAD4 exome AF: 0.00000547 AC: 6AN: 1097724Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 3AN XY: 363098
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GnomAD4 genome Cov.: 24
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Oct 13, 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
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at