chr6-34983365-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PM1PM2PP2BP4_Strong
The NM_015245.3(ANKS1A):c.952A>C(p.Thr318Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,609,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015245.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.952A>C | p.Thr318Pro | missense_variant | 7/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.952A>C | p.Thr318Pro | missense_variant | 7/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.1015A>C | p.Thr339Pro | missense_variant | 8/25 | P1 | |||
ANKS1A | ENST00000650178.1 | c.1015A>C | p.Thr339Pro | missense_variant | 8/10 |
Frequencies
GnomAD3 genomes ? AF: 0.0000270 AC: 4AN: 148390Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250824Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135560
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460804Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726690
GnomAD4 genome ? AF: 0.0000270 AC: 4AN: 148390Hom.: 0 Cov.: 32 AF XY: 0.0000554 AC XY: 4AN XY: 72210
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.952A>C (p.T318P) alteration is located in exon 7 (coding exon 7) of the ANKS1A gene. This alteration results from a A to C substitution at nucleotide position 952, causing the threonine (T) at amino acid position 318 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at