chr6-35017465-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015245.3(ANKS1A):c.1424-8A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000229 in 1,579,516 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, splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.1424-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.1424-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015245.3 | ||||
ANKS1A | ENST00000649117.1 | c.1487-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 151874Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000276 AC: 62AN: 224890Hom.: 0 AF XY: 0.000278 AC XY: 34AN XY: 122518
GnomAD4 exome AF: 0.000234 AC: 334AN: 1427642Hom.: 0 Cov.: 31 AF XY: 0.000229 AC XY: 162AN XY: 706440
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 151874Hom.: 0 Cov.: 32 AF XY: 0.000189 AC XY: 14AN XY: 74136
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at