rs2294208
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014227.3(SLC5A4):c.1449+23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 1,534,040 control chromosomes in the GnomAD database, including 166,117 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 0.51 ( 21069 hom., cov: 32)
Exomes 𝑓: 0.45 ( 145048 hom. )
Consequence
SLC5A4
NM_014227.3 intron
NM_014227.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.17
Genes affected
SLC5A4 (HGNC:11039): (solute carrier family 5 member 4) Predicted to enable glucose:sodium symporter activity and proton transmembrane transporter activity. Predicted to be involved in sodium ion transport. Predicted to act upstream of or within proton transmembrane transport. Predicted to be active in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A4 | NM_014227.3 | c.1449+23G>A | intron_variant | ENST00000266086.6 | |||
SLC5A4-AS1 | NR_149072.1 | n.274+18356C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A4 | ENST00000266086.6 | c.1449+23G>A | intron_variant | 1 | NM_014227.3 | P1 | |||
SLC5A4-AS1 | ENST00000452181.2 | n.274+18356C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
SLC5A4-AS1 | ENST00000434942.2 | n.225-3458C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.507 AC: 76908AN: 151834Hom.: 21027 Cov.: 32
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GnomAD3 exomes AF: 0.424 AC: 89678AN: 211306Hom.: 20528 AF XY: 0.426 AC XY: 49037AN XY: 115150
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GnomAD4 exome AF: 0.451 AC: 623226AN: 1382088Hom.: 145048 Cov.: 22 AF XY: 0.449 AC XY: 308359AN XY: 686826
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GnomAD4 genome ? AF: 0.507 AC: 77013AN: 151952Hom.: 21069 Cov.: 32 AF XY: 0.499 AC XY: 37039AN XY: 74288
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at