chr22-32231043-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014227.3(SLC5A4):c.1054G>A(p.Val352Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014227.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A4 | NM_014227.3 | c.1054G>A | p.Val352Met | missense_variant | 10/15 | ENST00000266086.6 | |
SLC5A4-AS1 | NR_149072.1 | n.274+23767C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A4 | ENST00000266086.6 | c.1054G>A | p.Val352Met | missense_variant | 10/15 | 1 | NM_014227.3 | P1 | |
SLC5A4-AS1 | ENST00000452181.2 | n.274+23767C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
SLC5A4-AS1 | ENST00000434942.2 | n.507+1671C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251334Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135812
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461638Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727146
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.1054G>A (p.V352M) alteration is located in exon 10 (coding exon 10) of the SLC5A4 gene. This alteration results from a G to A substitution at nucleotide position 1054, causing the valine (V) at amino acid position 352 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at