NM_000441.2:c.1708-18T>A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4BA1BP7
This summary comes from the ClinGen Evidence Repository: The filtering allele frequency (the lower threshold of the 95% CI of 1456/25104) of the c.1708-18T>A variant in the SLC26A4 gene is 5.55% for European (Finnish) chromosomes by gnomAD v2.1.1, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). This silent variant in SLC26A4 is not predicted by the computational prediction analysis using MaxEntScan to impact splicing (BP7, BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA4432923/MONDO:0010134/005
Frequency
Consequence
NM_000441.2 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A4 | ENST00000644269.2 | c.1708-18T>A | intron_variant | Intron 15 of 20 | NM_000441.2 | ENSP00000494017.1 | ||||
SLC26A4 | ENST00000480841.5 | n.557-18T>A | intron_variant | Intron 6 of 7 | 3 | |||||
SLC26A4 | ENST00000492030.2 | n.91-744T>A | intron_variant | Intron 1 of 5 | 5 | |||||
SLC26A4 | ENST00000644846.1 | n.418-18T>A | intron_variant | Intron 5 of 9 | ENSP00000494344.1 |
Frequencies
GnomAD3 genomes AF: 0.0236 AC: 3584AN: 152152Hom.: 74 Cov.: 32
GnomAD3 exomes AF: 0.0256 AC: 6412AN: 250804Hom.: 126 AF XY: 0.0249 AC XY: 3378AN XY: 135584
GnomAD4 exome AF: 0.0295 AC: 39493AN: 1338334Hom.: 682 Cov.: 21 AF XY: 0.0287 AC XY: 19299AN XY: 673334
GnomAD4 genome AF: 0.0236 AC: 3588AN: 152270Hom.: 74 Cov.: 32 AF XY: 0.0236 AC XY: 1756AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:5
- -
- -
- -
- -
- -
not provided Benign:5
- -
- -
- -
- -
This variant is associated with the following publications: (PMID: 23280318) -
Pendred syndrome Benign:2
The filtering allele frequency (the lower threshold of the 95% CI of 1456/25104) of the c.1708-18T>A variant in the SLC26A4 gene is 5.55% for European (Finnish) chromosomes by gnomAD v2.1.1, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). This silent variant in SLC26A4 is not predicted by the computational prediction analysis using MaxEntScan to impact splicing (BP7, BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4. -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at