7-69599761-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_015570(AUTS2):c.108C>G(p.Gly36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000528 in 151488 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Consequence
AUTS2
NM_015570 synonymous
NM_015570 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.402
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
Variant 7:69599761-C>G is Benign according to our data. Variant chr7-69599761-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 748288. Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.402 with no splicing effect.
BS2
?
High AC in GnomAd at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.108C>G | p.Gly36= | synonymous_variant | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.108C>G | p.Gly36= | synonymous_variant | 1/19 | 1 | NM_015570.4 | P4 | |
AUTS2 | ENST00000406775.6 | c.108C>G | p.Gly36= | synonymous_variant | 1/18 | 1 | |||
AUTS2 | ENST00000403018.3 | c.108C>G | p.Gly36= | synonymous_variant | 1/5 | 1 | |||
AUTS2 | ENST00000644939.1 | c.108C>G | p.Gly36= | synonymous_variant | 1/19 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151488Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 8.16e-7 AC: 1AN: 1225852Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 598942
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 04, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at