7-107701942-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_000441.2(SLC26A4):c.1919G>T(p.Trp640Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,460,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000441.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A4 | ENST00000644269.2 | c.1919G>T | p.Trp640Leu | missense_variant | Exon 17 of 21 | NM_000441.2 | ENSP00000494017.1 | |||
SLC26A4 | ENST00000492030.2 | n.206G>T | non_coding_transcript_exon_variant | Exon 2 of 6 | 5 | |||||
SLC26A4 | ENST00000644846.1 | n.629G>T | non_coding_transcript_exon_variant | Exon 7 of 10 | ENSP00000494344.1 | |||||
SLC26A4 | ENST00000480841.5 | n.*58G>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460958Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726858
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at