rs189357878
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000262320.8(AXIN1):c.2186+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,607,918 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000262320.8 splice_region, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AXIN1 | NM_003502.4 | c.2186+7C>T | splice_region_variant, intron_variant | ENST00000262320.8 | NP_003493.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AXIN1 | ENST00000262320.8 | c.2186+7C>T | splice_region_variant, intron_variant | 1 | NM_003502.4 | ENSP00000262320 | A1 | |||
AXIN1 | ENST00000354866.7 | c.2186+7C>T | splice_region_variant, intron_variant | 1 | ENSP00000346935 | P4 | ||||
AXIN1 | ENST00000457798.1 | c.49+7C>T | splice_region_variant, intron_variant | 3 | ENSP00000416835 | |||||
AXIN1 | ENST00000461023.5 | n.1490C>T | non_coding_transcript_exon_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00845 AC: 1286AN: 152168Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00945 AC: 2297AN: 242988Hom.: 16 AF XY: 0.0101 AC XY: 1343AN XY: 132808
GnomAD4 exome AF: 0.0116 AC: 16841AN: 1455632Hom.: 121 Cov.: 31 AF XY: 0.0118 AC XY: 8542AN XY: 724226
GnomAD4 genome AF: 0.00845 AC: 1287AN: 152286Hom.: 11 Cov.: 32 AF XY: 0.00829 AC XY: 617AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | AXIN1: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at