rs4326350
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173683.4(XKR6):c.962-7229G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,050 control chromosomes in the GnomAD database, including 19,067 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 0.48 ( 19067 hom., cov: 33)
Consequence
XKR6
NM_173683.4 intron
NM_173683.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.784
Genes affected
XKR6 (HGNC:27806): (XK related 6) Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XKR6 | NM_173683.4 | c.962-7229G>C | intron_variant | ENST00000416569.3 | |||
XKR6 | XM_024447129.2 | c.962-7130G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XKR6 | ENST00000416569.3 | c.962-7229G>C | intron_variant | 1 | NM_173683.4 | P1 | |||
XKR6 | ENST00000382461.8 | c.185-7229G>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.483 AC: 73366AN: 151932Hom.: 19045 Cov.: 33
GnomAD3 genomes
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151932
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.483 AC: 73425AN: 152050Hom.: 19067 Cov.: 33 AF XY: 0.471 AC XY: 35026AN XY: 74344
GnomAD4 genome
?
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73425
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152050
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33
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35026
AN XY:
74344
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Asia WGS
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891
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at