chr9-98736542-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_173551.5(ANKS6):c.2593C>T(p.Pro865Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000491 in 1,612,498 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_173551.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.2593C>T | p.Pro865Ser | missense_variant | Exon 15 of 15 | 1 | NM_173551.5 | ENSP00000297837.6 | ||
ANKS6 | ENST00000375019.6 | c.1690C>T | p.Pro564Ser | missense_variant | Exon 14 of 15 | 5 | ENSP00000364159.2 | |||
ANKS6 | ENST00000444472.5 | c.1000C>T | p.Pro334Ser | missense_variant | Exon 8 of 9 | 2 | ENSP00000398648.1 | |||
ANKS6 | ENST00000634393.1 | n.1728C>T | non_coding_transcript_exon_variant | Exon 14 of 15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000578 AC: 88AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00113 AC: 280AN: 247076Hom.: 3 AF XY: 0.00114 AC XY: 153AN XY: 134140
GnomAD4 exome AF: 0.000482 AC: 704AN: 1460226Hom.: 7 Cov.: 32 AF XY: 0.000486 AC XY: 353AN XY: 726106
GnomAD4 genome AF: 0.000578 AC: 88AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1
The P865S variant in the ANKS6 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. Although not present in the homozygous state, the P865S variant was observed on 97 of 7922 alleles (1.2%) from individuals of East Asian background, in the Exome Aggregation Consortium (ExAC) data set, indicating it may be a rare variant in this population. The P865S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution also occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret P865S as a variant of uncertain significance. -
Nephronophthisis 16 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at