7-101156606-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_001283.5(AP1S1):c.16C>T(p.Leu6Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,611,992 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L6L) has been classified as Likely benign.
Frequency
Consequence
NM_001283.5 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP1S1 | NM_001283.5 | c.16C>T | p.Leu6Leu | synonymous_variant | Exon 2 of 5 | ENST00000337619.11 | NP_001274.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 40AN: 245648Hom.: 0 AF XY: 0.0000751 AC XY: 10AN XY: 133174
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1459660Hom.: 1 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 725814
GnomAD4 genome AF: 0.000525 AC: 80AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at