2-44942162-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005413.4(SIX3):c.58G>T(p.Ala20Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,598,064 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A20A) has been classified as Likely benign.
Frequency
Consequence
NM_005413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIX3 | NM_005413.4 | c.58G>T | p.Ala20Ser | missense_variant | 1/2 | ENST00000260653.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIX3 | ENST00000260653.5 | c.58G>T | p.Ala20Ser | missense_variant | 1/2 | 1 | NM_005413.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000924 AC: 14AN: 151564Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000486 AC: 114AN: 234552Hom.: 3 AF XY: 0.000646 AC XY: 83AN XY: 128428
GnomAD4 exome AF: 0.000216 AC: 313AN: 1446384Hom.: 6 Cov.: 32 AF XY: 0.000318 AC XY: 229AN XY: 719914
GnomAD4 genome ? AF: 0.0000923 AC: 14AN: 151680Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 74068
ClinVar
Submissions by phenotype
Holoprosencephaly 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | SIX3: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at