chr20-3227872-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_001174089.2(SLC4A11):c.2559-16C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000621 in 1,609,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
SLC4A11
NM_001174089.2 splice_polypyrimidine_tract, intron
NM_001174089.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.568
Genes affected
SLC4A11 (HGNC:16438): (solute carrier family 4 member 11) This gene encodes a voltage-regulated, electrogenic sodium-coupled borate cotransporter that is essential for borate homeostasis, cell growth and cell proliferation. Mutations in this gene have been associated with a number of endothelial corneal dystrophies including recessive corneal endothelial dystrophy 2, corneal dystrophy and perceptive deafness, and Fuchs endothelial corneal dystrophy. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 20-3227872-G-A is Benign according to our data. Variant chr20-3227872-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2978380.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 7 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A11 | NM_001174089.2 | c.2559-16C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000642402.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A11 | ENST00000642402.1 | c.2559-16C>T | splice_polypyrimidine_tract_variant, intron_variant | NM_001174089.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000816 AC: 2AN: 245004Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132744
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GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457664Hom.: 0 Cov.: 30 AF XY: 0.00000690 AC XY: 5AN XY: 725046
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74280
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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 | Invitae | Dec 27, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at