rs568363861
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_028137.1(SLC26A4-AS1):n.198-496C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 152,336 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Consequence
SLC26A4-AS1
NR_028137.1 intron, non_coding_transcript
NR_028137.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.478
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A4-AS1 | NR_028137.1 | n.198-496C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A4-AS1 | ENST00000668981.1 | n.257+900C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152218Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 0
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GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74496
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 22, 2017 | The c.-157G>A variant in SLC26A4 has not been previously reported in individuals with hearing loss, but has been identified in 0.1% (1/838) of Latino chromosome s by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs568363861). Although this variant has been seen in the general populatio n, its frequency is not high enough to rule out a pathogenic role. This variant is in the 5' untranslated region (UTR) of the SLC26A4 gene. It is unknown and c annot be predicted whether or not this variant impacts the protein. In summary, the clinical significance of this variant is uncertain. - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at