chr16-55656812-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_001172501.3(SLC6A2):c.118A>T(p.Asn40Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00013 in 1,613,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. N40N) has been classified as Likely benign.
Frequency
Consequence
NM_001172501.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A2 | NM_001172501.3 | c.118A>T | p.Asn40Tyr | missense_variant | 2/15 | ENST00000568943.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A2 | ENST00000568943.6 | c.118A>T | p.Asn40Tyr | missense_variant | 2/15 | 1 | NM_001172501.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 249272Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134990
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461166Hom.: 0 Cov.: 32 AF XY: 0.000131 AC XY: 95AN XY: 726898
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.118A>T (p.N40Y) alteration is located in exon 1 (coding exon 1) of the SLC6A2 gene. This alteration results from a A to T substitution at nucleotide position 118, causing the asparagine (N) at amino acid position 40 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