rs4973768
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001321103.2(SLC4A7):c.*2242G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,260 control chromosomes in the GnomAD database, including 15,155 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 15123 hom., cov: 33)
Exomes 𝑓: 0.40 ( 32 hom. )
Consequence
SLC4A7
NM_001321103.2 3_prime_UTR
NM_001321103.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.40
Genes affected
SLC4A7 (HGNC:11033): (solute carrier family 4 member 7) This locus encodes a sodium bicarbonate cotransporter. The encoded transmembrane protein appears to transport sodium and bicarbonate ions in a 1:1 ratio, and is thus considered an electroneutral cotransporter. The encoded protein likely plays a critical role in regulation of intracellular pH involved in visual and auditory sensory transmission. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC4A7 | NM_001321103.2 | c.*2242G>A | 3_prime_UTR_variant | 26/26 | ENST00000454389.6 | NP_001308032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC4A7 | ENST00000454389.6 | c.*2242G>A | 3_prime_UTR_variant | 26/26 | 1 | NM_001321103.2 | ENSP00000390394 | |||
ENST00000661166.1 | n.975+3980C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.440 AC: 66738AN: 151730Hom.: 15122 Cov.: 33
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GnomAD4 exome AF: 0.402 AC: 165AN: 410Hom.: 32 Cov.: 0 AF XY: 0.360 AC XY: 90AN XY: 250
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GnomAD4 genome AF: 0.440 AC: 66758AN: 151850Hom.: 15123 Cov.: 33 AF XY: 0.440 AC XY: 32658AN XY: 74202
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ClinVar
Not reported inComputational 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