chr3-38376154-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005108.4(XYLB):āc.1042A>Gā(p.Asn348Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00531 in 1,614,086 control chromosomes in the GnomAD database, including 315 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005108.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLB | NM_005108.4 | c.1042A>G | p.Asn348Asp | missense_variant | 13/19 | ENST00000207870.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLB | ENST00000207870.8 | c.1042A>G | p.Asn348Asp | missense_variant | 13/19 | 1 | NM_005108.4 | P1 | |
XYLB | ENST00000650590.1 | c.961A>G | p.Asn321Asp | missense_variant | 12/18 | ||||
XYLB | ENST00000424034.5 | c.*705A>G | 3_prime_UTR_variant, NMD_transcript_variant | 11/17 | 2 | ||||
XYLB | ENST00000649234.1 | c.*277A>G | 3_prime_UTR_variant, NMD_transcript_variant | 14/20 |
Frequencies
GnomAD3 genomes AF: 0.0265 AC: 4032AN: 152160Hom.: 170 Cov.: 32
GnomAD3 exomes AF: 0.00733 AC: 1844AN: 251466Hom.: 64 AF XY: 0.00562 AC XY: 764AN XY: 135910
GnomAD4 exome AF: 0.00310 AC: 4537AN: 1461808Hom.: 145 Cov.: 30 AF XY: 0.00280 AC XY: 2039AN XY: 727206
GnomAD4 genome AF: 0.0265 AC: 4035AN: 152278Hom.: 170 Cov.: 32 AF XY: 0.0254 AC XY: 1888AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at