7-107701087-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000441.2(SLC26A4):c.1708-14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000784 in 1,531,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000441.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A4 | ENST00000644269.2 | c.1708-14A>G | intron_variant | Intron 15 of 20 | NM_000441.2 | ENSP00000494017.1 | ||||
SLC26A4 | ENST00000480841.5 | n.557-14A>G | intron_variant | Intron 6 of 7 | 3 | |||||
SLC26A4 | ENST00000492030.2 | n.91-740A>G | intron_variant | Intron 1 of 5 | 5 | |||||
SLC26A4 | ENST00000644846.1 | n.418-14A>G | intron_variant | Intron 5 of 9 | ENSP00000494344.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000798 AC: 11AN: 1379184Hom.: 0 Cov.: 23 AF XY: 0.00000723 AC XY: 5AN XY: 691402
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant classified as Uncertain Significance - Favor Benign. The c.1708-14A>G va riant in SLC26A4 has not been previously reported in individuals with hearing lo ss or in large population studies. This variant is located in the 3' splice regi on. Computational tools do not suggest an impact to splicing. However, this info rmation is not predictive enough to rule out pathogenicity. In summary, while th e clinical significance of the c.1708-14A>G variant is uncertain, these data sug gest that it is more likely to be benign. ACMG/AMP Criteria applied: PM2, BP7. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at