rs35866044

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_133478.3(SLC4A5):​c.893dupT​(p.Lys300GlnfsTer60) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC4A5
NM_133478.3 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 9.28
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC4A5NM_133478.3 linkc.893dupT p.Lys300GlnfsTer60 frameshift_variant Exon 13 of 31 ENST00000394019.7 NP_597812.1 Q9BY07-3
SLC4A5NM_021196.3 linkc.893dupT p.Lys300GlnfsTer60 frameshift_variant Exon 8 of 26 NP_067019.3 Q9BY07-1
SLC4A5NM_001386136.1 linkc.545dupT p.Lys184GlnfsTer60 frameshift_variant Exon 7 of 25 NP_001373065.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC4A5ENST00000394019.7 linkc.893dupT p.Lys300GlnfsTer60 frameshift_variant Exon 13 of 31 5 NM_133478.3 ENSP00000377587.2 Q9BY07-3
ENSG00000264324ENST00000451608.2 linkn.*1481dupT non_coding_transcript_exon_variant Exon 18 of 39 5 ENSP00000416453.2 E7EWF7
ENSG00000264324ENST00000451608.2 linkn.*1481dupT 3_prime_UTR_variant Exon 18 of 39 5 ENSP00000416453.2 E7EWF7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35866044; hg19: chr2-74483033; API