rs144531370
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_022166.4(XYLT1):c.1272G>A(p.Ala424=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000753 in 1,614,126 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A424A) has been classified as Likely benign.
Frequency
Consequence
NM_022166.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLT1 | NM_022166.4 | c.1272G>A | p.Ala424= | synonymous_variant | 5/12 | ENST00000261381.7 | |
XYLT1 | XM_047434458.1 | c.1233G>A | p.Ala411= | synonymous_variant | 4/11 | ||
XYLT1 | XM_017023539.3 | c.1272G>A | p.Ala424= | synonymous_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLT1 | ENST00000261381.7 | c.1272G>A | p.Ala424= | synonymous_variant | 5/12 | 1 | NM_022166.4 | P1 | |
XYLT1 | ENST00000575674.1 | n.400G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000572 AC: 87AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00130 AC: 326AN: 249980Hom.: 3 AF XY: 0.00163 AC XY: 221AN XY: 135188
GnomAD4 exome AF: 0.000774 AC: 1131AN: 1461842Hom.: 14 Cov.: 32 AF XY: 0.000997 AC XY: 725AN XY: 727218
GnomAD4 genome ? AF: 0.000558 AC: 85AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74464
ClinVar
Submissions by phenotype
Desbuquois dysplasia 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | XYLT1: BP4, BP7, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at