rs759458
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003038.5(SLC1A4):c.1195G>A(p.Val399Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,613,822 control chromosomes in the GnomAD database, including 51,425 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. V399V) has been classified as Likely benign.
Frequency
Consequence
NM_003038.5 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 |
---|---|---|---|---|---|---|---|
SLC1A4 | NM_003038.5 | c.1195G>A | p.Val399Ile | missense_variant | 6/8 | ENST00000234256.4 | |
SLC1A4 | NM_001348406.2 | c.535G>A | p.Val179Ile | missense_variant | 6/8 | ||
SLC1A4 | NM_001348407.2 | c.535G>A | p.Val179Ile | missense_variant | 6/8 | ||
SLC1A4 | NM_001193493.2 | c.301G>A | p.Val101Ile | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC1A4 | ENST00000234256.4 | c.1195G>A | p.Val399Ile | missense_variant | 6/8 | 1 | NM_003038.5 | P1 | |
LINC02245 | ENST00000653778.1 | n.513+29723C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.221 AC: 33569AN: 151964Hom.: 3938 Cov.: 32
GnomAD3 exomes AF: 0.235 AC: 58965AN: 251332Hom.: 7494 AF XY: 0.247 AC XY: 33490AN XY: 135820
GnomAD4 exome AF: 0.251 AC: 367174AN: 1461740Hom.: 47489 Cov.: 34 AF XY: 0.254 AC XY: 184843AN XY: 727170
GnomAD4 genome ? AF: 0.221 AC: 33573AN: 152082Hom.: 3936 Cov.: 32 AF XY: 0.218 AC XY: 16171AN XY: 74316
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at