chr6-34967239-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015245.3(ANKS1A):c.198C>T(p.Ser66=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015245.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.198C>T | p.Ser66= | splice_region_variant, synonymous_variant | 2/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.198C>T | p.Ser66= | splice_region_variant, synonymous_variant | 2/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.198C>T | p.Ser66= | splice_region_variant, synonymous_variant | 2/25 | P1 | |||
ANKS1A | ENST00000650178.1 | c.198C>T | p.Ser66= | splice_region_variant, synonymous_variant | 2/10 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151542Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250358Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135322
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460728Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726720
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151542Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73940
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at