chr3-10819744-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014229.3(SLC6A11):c.424C>T(p.His142Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014229.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A11 | NM_014229.3 | c.424C>T | p.His142Tyr | missense_variant | 3/14 | ENST00000254488.7 | NP_055044.1 | |
SLC6A11 | NM_001317406.3 | c.424C>T | p.His142Tyr | missense_variant | 3/4 | NP_001304335.1 | ||
SLC6A11 | XM_011534033.3 | c.424C>T | p.His142Tyr | missense_variant | 3/9 | XP_011532335.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A11 | ENST00000254488.7 | c.424C>T | p.His142Tyr | missense_variant | 3/14 | 1 | NM_014229.3 | ENSP00000254488 | P1 | |
SLC6A11 | ENST00000454147.1 | c.424C>T | p.His142Tyr | missense_variant | 3/4 | 1 | ENSP00000404120 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251434Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135886
GnomAD4 exome AF: 0.000133 AC: 195AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.000139 AC XY: 101AN XY: 727232
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.424C>T (p.H142Y) alteration is located in exon 3 (coding exon 3) of the SLC6A11 gene. This alteration results from a C to T substitution at nucleotide position 424, causing the histidine (H) at amino acid position 142 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at