chr5-149980602-C-CTTG
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP3
The NM_000112.4(SLC26A2):c.1020_1022dup(p.Val340dup) variant causes a inframe insertion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,782 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L337L) has been classified as Likely benign.
Frequency
Consequence
NM_000112.4 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A2 | NM_000112.4 | c.1020_1022dup | p.Val340dup | inframe_insertion | 3/3 | ENST00000286298.5 | |
SLC26A2 | XM_017009191.3 | c.1020_1022dup | p.Val340dup | inframe_insertion | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A2 | ENST00000286298.5 | c.1020_1022dup | p.Val340dup | inframe_insertion | 3/3 | 1 | NM_000112.4 | P1 | |
SLC26A2 | ENST00000503336.1 | c.372+2262_372+2264dup | intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251132Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135730
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461782Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727206
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Diastrophic dysplasia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics | Apr 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at