chr20-3228242-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001174089.2(SLC4A11):c.2558+17A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00199 in 1,520,830 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0085 ( 21 hom., cov: 28)
Exomes 𝑓: 0.0013 ( 21 hom. )
Consequence
SLC4A11
NM_001174089.2 intron
NM_001174089.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.428
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 20-3228242-T-A is Benign according to our data. Variant chr20-3228242-T-A is described in ClinVar as [Benign]. Clinvar id is 1596059.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00847 (1184/139830) while in subpopulation AFR AF= 0.0268 (1007/37570). AF 95% confidence interval is 0.0254. There are 21 homozygotes in gnomad4. There are 530 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1179 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A11 | NM_001174089.2 | c.2558+17A>T | intron_variant | ENST00000642402.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A11 | ENST00000642402.1 | c.2558+17A>T | intron_variant | NM_001174089.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00844 AC: 1179AN: 139766Hom.: 21 Cov.: 28
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GnomAD3 exomes AF: 0.00232 AC: 576AN: 247882Hom.: 8 AF XY: 0.00158 AC XY: 213AN XY: 134700
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GnomAD4 exome AF: 0.00134 AC: 1849AN: 1381000Hom.: 21 Cov.: 36 AF XY: 0.00121 AC XY: 831AN XY: 686322
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GnomAD4 genome ? AF: 0.00847 AC: 1184AN: 139830Hom.: 21 Cov.: 28 AF XY: 0.00783 AC XY: 530AN XY: 67678
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at