chr7-107660793-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NR_028137.1(SLC26A4-AS1):n.198-587G>A 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 0.0000591 in 152,240 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC26A4-AS1
NR_028137.1 intron, non_coding_transcript
NR_028137.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.122
Genes affected
SLC26A4-AS1 (HGNC:22385): (SLC26A4 antisense RNA 1)
SLC26A4 (HGNC:8818): (solute carrier family 26 member 4) Mutations in this gene are associated with Pendred syndrome, the most common form of syndromic deafness, an autosomal-recessive disease. It is highly homologous to the SLC26A3 gene; they have similar genomic structures and this gene is located 3' of the SLC26A3 gene. The encoded protein has homology to sulfate transporters. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 7-107660793-C-T is Benign according to our data. Variant chr7-107660793-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 43488.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A4-AS1 | NR_028137.1 | n.198-587G>A | intron_variant, non_coding_transcript_variant | ||||
SLC26A4 | NM_000441.2 | upstream_gene_variant | ENST00000644269.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A4-AS1 | ENST00000668981.1 | n.257+809G>A | intron_variant, non_coding_transcript_variant | ||||||
SLC26A4 | ENST00000644269.2 | upstream_gene_variant | NM_000441.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152122Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 38Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 32
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 20, 2012 | The -66C>T variant in the 5?UTR of SLC26A4: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not l ocated within a splice consensus sequence, and another base change at this site, -66C>G, has been observed as a common benign variant (rs17154282). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at