chr7-101156606-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The ENST00000337619.11(AP1S1):c.16C>T(p.Leu6=) 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
ENST00000337619.11 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP1S1 | NM_001283.5 | c.16C>T | p.Leu6= | synonymous_variant | 2/5 | ENST00000337619.11 | NP_001274.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AP1S1 | ENST00000337619.11 | c.16C>T | p.Leu6= | synonymous_variant | 2/5 | 1 | NM_001283.5 | ENSP00000336666 | P4 |
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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at