chr2-161708815-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001178015.2(SLC4A10):c.49-62158T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,532,466 control chromosomes in the GnomAD database, including 167 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 93 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 74 hom. )
Consequence
SLC4A10
NM_001178015.2 intron
NM_001178015.2 intron
Scores
2
12
Clinical Significance
Conservation
PhyloP100: 3.58
Genes affected
SLC4A10 (HGNC:13811): (solute carrier family 4 member 10) This gene belongs to a small family of sodium-coupled bicarbonate transporters (NCBTs) that regulate the intracellular pH of neurons, the secretion of bicarbonate ions across the choroid plexus, and the pH of the brain extracellular fluid. The protein encoded by this gene was initially identified as a sodium-driven chloride bicarbonate exchanger (NCBE) though there is now evidence that its sodium/bicarbonate cotransport activity is independent of any chloride ion countertransport under physiological conditions. This gene is now classified as a member A10 of the SLC4 family of transmembrane solute carriers. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 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 (MetaRNN=0.0021554232).
BP6
Variant 2-161708815-T-G is Benign according to our data. Variant chr2-161708815-T-G is described in ClinVar as [Benign]. Clinvar id is 3038020.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A10 | NM_001178015.2 | c.49-62158T>G | intron_variant | ENST00000446997.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A10 | ENST00000446997.6 | c.49-62158T>G | intron_variant | 1 | NM_001178015.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0185 AC: 2800AN: 151538Hom.: 91 Cov.: 32
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GnomAD3 exomes AF: 0.00340 AC: 454AN: 133368Hom.: 14 AF XY: 0.00257 AC XY: 187AN XY: 72682
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GnomAD4 exome AF: 0.00188 AC: 2597AN: 1380810Hom.: 74 Cov.: 30 AF XY: 0.00170 AC XY: 1161AN XY: 681346
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GnomAD4 genome AF: 0.0185 AC: 2806AN: 151656Hom.: 93 Cov.: 32 AF XY: 0.0176 AC XY: 1306AN XY: 74142
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC4A10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
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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