chr12-102958382-A-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004316.4(ASCL1):c.138A>T(p.Ala46Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0062 in 1,470,852 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004316.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASCL1 | ENST00000266744.4 | c.138A>T | p.Ala46Ala | synonymous_variant | Exon 1 of 2 | 1 | NM_004316.4 | ENSP00000266744.3 | ||
PAH | ENST00000547319.1 | n.29T>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 4 | |||||
PAH | ENST00000551337.5 | c.-283T>A | upstream_gene_variant | 3 | ENSP00000447620.1 |
Frequencies
GnomAD3 genomes AF: 0.00455 AC: 674AN: 148132Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00475 AC: 399AN: 84078Hom.: 0 AF XY: 0.00431 AC XY: 207AN XY: 47986
GnomAD4 exome AF: 0.00638 AC: 8441AN: 1322612Hom.: 37 Cov.: 29 AF XY: 0.00614 AC XY: 4001AN XY: 652032
GnomAD4 genome AF: 0.00455 AC: 674AN: 148240Hom.: 3 Cov.: 33 AF XY: 0.00439 AC XY: 318AN XY: 72480
ClinVar
Submissions by phenotype
not provided Benign:2
ASCL1: BP4, BP7, BS2 -
- -
not specified Benign:1
p.Ala46Ala in exon 1 of ASCL1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 0.2% (5/2136) of Eu ropean chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadi nstitute.org; dbSNP rs552552603). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at