7-69598673-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_015570.4(AUTS2):c.-981T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00357 in 159,586 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 30)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
AUTS2
NM_015570.4 5_prime_UTR
NM_015570.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.378
Genes affected
AUTS2 (HGNC:14262): (activator of transcription and developmental regulator AUTS2) This gene has been implicated in neurodevelopment and as a candidate gene for numerous neurological disorders, including autism spectrum disorders, intellectual disability, and developmental delay. Mutations in this gene have also been associated with non-neurological disorders, such as acute lymphoblastic leukemia, aging of the skin, early-onset androgenetic alopecia, and certain cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 7-69598673-T-C is Benign according to our data. Variant chr7-69598673-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1199522.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00374 (569/152136) while in subpopulation AFR AF= 0.00994 (413/41542). AF 95% confidence interval is 0.00915. There are 3 homozygotes in gnomad4. There are 280 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 569 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.-981T>C | 5_prime_UTR_variant | 1/19 | ENST00000342771.10 | NP_056385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.-981T>C | 5_prime_UTR_variant | 1/19 | 1 | NM_015570.4 | ENSP00000344087 | P4 | ||
AUTS2 | ENST00000644939.1 | c.-981T>C | 5_prime_UTR_variant | 1/19 | ENSP00000496726 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00372 AC: 565AN: 152026Hom.: 3 Cov.: 30
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GnomAD4 exome AF: 0.000134 AC: 1AN: 7450Hom.: 0 Cov.: 0 AF XY: 0.000187 AC XY: 1AN XY: 5360
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GnomAD4 genome AF: 0.00374 AC: 569AN: 152136Hom.: 3 Cov.: 30 AF XY: 0.00376 AC XY: 280AN XY: 74374
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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 | GeneDx | Jun 24, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at