NM_015570.4:c.11C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015570.4(AUTS2):c.11C>T(p.Pro4Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0046 in 1,304,368 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015570.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AUTS2 | NM_015570.4 | c.11C>T | p.Pro4Leu | missense_variant | Exon 1 of 19 | ENST00000342771.10 | NP_056385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AUTS2 | ENST00000342771.10 | c.11C>T | p.Pro4Leu | missense_variant | Exon 1 of 19 | 1 | NM_015570.4 | ENSP00000344087.4 | ||
AUTS2 | ENST00000406775.6 | c.11C>T | p.Pro4Leu | missense_variant | Exon 1 of 18 | 1 | ENSP00000385263.2 | |||
AUTS2 | ENST00000403018.3 | c.11C>T | p.Pro4Leu | missense_variant | Exon 1 of 5 | 1 | ENSP00000385572.2 | |||
AUTS2 | ENST00000644939.1 | c.11C>T | p.Pro4Leu | missense_variant | Exon 1 of 19 | ENSP00000496726.1 |
Frequencies
GnomAD3 genomes AF: 0.00289 AC: 440AN: 152036Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00341 AC: 38AN: 11154Hom.: 1 AF XY: 0.00368 AC XY: 22AN XY: 5974
GnomAD4 exome AF: 0.00483 AC: 5563AN: 1152222Hom.: 22 Cov.: 32 AF XY: 0.00471 AC XY: 2610AN XY: 554422
GnomAD4 genome AF: 0.00289 AC: 440AN: 152146Hom.: 2 Cov.: 32 AF XY: 0.00238 AC XY: 177AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:5
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This variant has been identified by standard clinical testing. -
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AUTS2: PP2, BS1, BS2 -
AUTS2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Intellectual disability Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at