12-102958344-ACGGCCGCAGCCGCGG-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BS1_SupportingBS2
The NM_004316.4(ASCL1):c.114_128del(p.Ala43_Ala47del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00189 in 1,452,160 control chromosomes in the GnomAD database, including 41 homozygotes. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. TAAAA34T) has been classified as Uncertain significance.
Frequency
Consequence
NM_004316.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASCL1 | NM_004316.4 | c.114_128del | p.Ala43_Ala47del | inframe_deletion | 1/2 | ENST00000266744.4 | |
PAH | NM_001354304.2 | c.-260_-246del | 5_prime_UTR_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASCL1 | ENST00000266744.4 | c.114_128del | p.Ala43_Ala47del | inframe_deletion | 1/2 | 1 | NM_004316.4 | P1 | |
PAH | ENST00000551337.5 | c.-260_-246del | 5_prime_UTR_variant | 1/5 | 3 | ||||
PAH | ENST00000547319.1 | n.52_66del | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00512 AC: 775AN: 151432Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00222 AC: 150AN: 67458Hom.: 14 AF XY: 0.00245 AC XY: 97AN XY: 39616
GnomAD4 exome AF: 0.00151 AC: 1968AN: 1300622Hom.: 39 AF XY: 0.00150 AC XY: 960AN XY: 640824
GnomAD4 genome AF: 0.00510 AC: 773AN: 151538Hom.: 2 Cov.: 32 AF XY: 0.00520 AC XY: 385AN XY: 74078
ClinVar
Submissions by phenotype
Congenital central hypoventilation Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Dec 01, 2003 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at