10-80157634-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_145868.2(ANXA11):c.1458+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,611,690 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
NM_145868.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA11 | NM_145868.2 | c.1458+7G>A | splice_region_variant, intron_variant | ENST00000422982.8 | NP_665875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA11 | ENST00000422982.8 | c.1458+7G>A | splice_region_variant, intron_variant | 1 | NM_145868.2 | ENSP00000404412 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000602 AC: 15AN: 249268Hom.: 0 AF XY: 0.0000742 AC XY: 10AN XY: 134712
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1459600Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 725950
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74296
ClinVar
Submissions by phenotype
ANXA11-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at