rs2070159
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001673.5(ASNS):c.829G>A(p.Ala277Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,614,120 control chromosomes in the GnomAD database, including 39 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A277A) has been classified as Likely benign.
Frequency
Consequence
NM_001673.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASNS | NM_001673.5 | c.829G>A | p.Ala277Thr | missense_variant | 7/13 | ENST00000394308.8 | |
CZ1P-ASNS | NR_147989.1 | n.2458G>A | non_coding_transcript_exon_variant | 13/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASNS | ENST00000394308.8 | c.829G>A | p.Ala277Thr | missense_variant | 7/13 | 1 | NM_001673.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00936 AC: 1424AN: 152168Hom.: 18 Cov.: 32
GnomAD3 exomes AF: 0.00252 AC: 634AN: 251402Hom.: 10 AF XY: 0.00188 AC XY: 255AN XY: 135880
GnomAD4 exome AF: 0.00100 AC: 1467AN: 1461834Hom.: 22 Cov.: 30 AF XY: 0.000914 AC XY: 665AN XY: 727226
GnomAD4 genome ? AF: 0.00935 AC: 1424AN: 152286Hom.: 17 Cov.: 32 AF XY: 0.00933 AC XY: 695AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 31, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 23, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at