rs3803957
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001174089.2(SLC4A11):c.89-8G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,613,366 control chromosomes in the GnomAD database, including 67,813 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 Benign (★★).
Frequency
Consequence
NM_001174089.2 splice_region, splice_polypyrimidine_tract, 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC4A11 | NM_001174089.2 | c.89-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000642402.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A11 | ENST00000642402.1 | c.89-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001174089.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.280 AC: 42499AN: 151936Hom.: 6148 Cov.: 32
GnomAD3 exomes AF: 0.306 AC: 76467AN: 249978Hom.: 12244 AF XY: 0.302 AC XY: 40918AN XY: 135378
GnomAD4 exome AF: 0.287 AC: 419874AN: 1461314Hom.: 61662 Cov.: 41 AF XY: 0.287 AC XY: 208652AN XY: 726912
GnomAD4 genome ? AF: 0.280 AC: 42513AN: 152052Hom.: 6151 Cov.: 32 AF XY: 0.287 AC XY: 21312AN XY: 74298
ClinVar
Submissions by phenotype
Corneal dystrophy-perceptive deafness syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 19, 2019 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 01, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Corneal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Congenital hereditary endothelial dystrophy of cornea Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at