chr3-10934147-T-C
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014229.3(SLC6A11):c.1556T>C(p.Met519Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,613,182 control chromosomes in the GnomAD database, including 55 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_014229.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A11 | ENST00000254488.7 | c.1556T>C | p.Met519Thr | missense_variant | Exon 12 of 14 | 1 | NM_014229.3 | ENSP00000254488.2 | ||
SLC6A11 | ENST00000464828.1 | n.182T>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
ENSG00000286962 | ENST00000656787.1 | n.350+2843A>G | intron_variant | Intron 3 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1578AN: 152196Hom.: 28 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00253 AC: 636AN: 251372 AF XY: 0.00203 show subpopulations
GnomAD4 exome AF: 0.00106 AC: 1545AN: 1460868Hom.: 27 Cov.: 30 AF XY: 0.000947 AC XY: 688AN XY: 726856 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0104 AC: 1583AN: 152314Hom.: 28 Cov.: 32 AF XY: 0.00964 AC XY: 718AN XY: 74472 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at