8-11200694-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_173683.4(XKR6):c.646G>A(p.Ala216Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,570,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173683.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XKR6 | NM_173683.4 | c.646G>A | p.Ala216Thr | missense_variant | 1/3 | ENST00000416569.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XKR6 | ENST00000416569.3 | c.646G>A | p.Ala216Thr | missense_variant | 1/3 | 1 | NM_173683.4 | P1 | |
XKR6 | ENST00000297303.4 | c.646G>A | p.Ala216Thr | missense_variant | 1/2 | 1 | |||
XKR6 | ENST00000529336.1 | c.142G>A | p.Ala48Thr | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 151796Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000230 AC: 42AN: 182692Hom.: 0 AF XY: 0.000250 AC XY: 26AN XY: 103878
GnomAD4 exome AF: 0.000171 AC: 242AN: 1419132Hom.: 0 Cov.: 32 AF XY: 0.000177 AC XY: 125AN XY: 705866
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 151796Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74144
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.646G>A (p.A216T) alteration is located in exon 1 (coding exon 1) of the XKR6 gene. This alteration results from a G to A substitution at nucleotide position 646, causing the alanine (A) at amino acid position 216 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at