7-69598914-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015570(AUTS2):c.-740T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151680 control chromosomes in the gnomAD Genomes database, including 5597 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5597 hom., cov: 30)
Consequence
AUTS2
NM_015570 5_prime_UTR
NM_015570 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.158
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 7:69598914-T>G is Benign according to our data. Variant chr7-69598914-T-G is described in ClinVar as [Benign]. Clinvar id is 1226087. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.-740T>G | 5_prime_UTR_variant | 1/19 | ENST00000342771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.-740T>G | 5_prime_UTR_variant | 1/19 | 1 | NM_015570.4 | P4 | ||
AUTS2 | ENST00000644939.1 | c.-740T>G | 5_prime_UTR_variant | 1/19 | A1 | ||||
AUTS2 | ENST00000406775.6 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.253 AC: 38371AN: 151680Hom.: 5597 Cov.: 30
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GnomAD4 exome AF: 0.228 AC: 443AN: 1942Hom.: 68 AF XY: 0.225 AC XY: 338AN XY: 1502
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 26, 2018 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at