chr3-195069812-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152531.5(XXYLT1):c.1085A>C(p.Asp362Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,613,956 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D362E) has been classified as Uncertain significance.
Frequency
Consequence
NM_152531.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XXYLT1 | NM_152531.5 | c.1085A>C | p.Asp362Ala | missense_variant | 4/4 | ENST00000310380.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XXYLT1 | ENST00000310380.11 | c.1085A>C | p.Asp362Ala | missense_variant | 4/4 | 1 | NM_152531.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249428Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135364
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461834Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727222
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152122Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.1085A>C (p.D362A) alteration is located in exon 4 (coding exon 4) of the XXYLT1 gene. This alteration results from a A to C substitution at nucleotide position 1085, causing the aspartic acid (D) at amino acid position 362 to be replaced by an alanine (A). 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