11-35260949-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004171.4(SLC1A2):c.1670A>G(p.Asn557Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000359 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/14 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. N557N) has been classified as Likely benign.
Frequency
Consequence
NM_004171.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC1A2 | NM_004171.4 | c.1670A>G | p.Asn557Ser | missense_variant | 11/11 | ENST00000278379.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC1A2 | ENST00000278379.9 | c.1670A>G | p.Asn557Ser | missense_variant | 11/11 | 1 | NM_004171.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251428Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135882
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461448Hom.: 0 Cov.: 29 AF XY: 0.0000316 AC XY: 23AN XY: 727082
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at