rs7571842
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_133478.3(SLC4A5):c.2434-214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,014 control chromosomes in the GnomAD database, including 22,337 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.53 ( 22337 hom., cov: 32)
Consequence
SLC4A5
NM_133478.3 intron
NM_133478.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.623
Genes affected
SLC4A5 (HGNC:18168): (solute carrier family 4 member 5) This gene encodes a member of the sodium bicarbonate cotransporter (NBC) family, part of the bicarbonate transporter superfamily. Sodium bicarbonate cotransporters are involved in intracellular pH regulation and electroneural or electrogenic sodium bicarbonate transport. This protein is thought to be an integral membrane protein. Multiple transcript variants encoding different isoforms have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
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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=-0.92).
BP6
?
Variant 2-74233777-A-G is Benign according to our data. Variant chr2-74233777-A-G is described in ClinVar as [Benign]. Clinvar id is 1235516.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A5 | NM_133478.3 | c.2434-214T>C | intron_variant | ENST00000394019.7 | |||
SLC4A5 | NM_001386136.1 | c.2086-214T>C | intron_variant | ||||
SLC4A5 | NM_021196.3 | c.2434-214T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A5 | ENST00000394019.7 | c.2434-214T>C | intron_variant | 5 | NM_133478.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.533 AC: 81017AN: 151892Hom.: 22308 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.533 AC: 81096AN: 152014Hom.: 22337 Cov.: 32 AF XY: 0.536 AC XY: 39854AN XY: 74312
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Asia WGS
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1790
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3478
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 | GeneDx | Feb 25, 2021 | This variant is associated with the following publications: (PMID: 29642240) - |
Computational scores
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Name
Calibrated prediction
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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