chr7-107661378-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000441.2(SLC26A4):c.-3-261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0246 in 579,984 control chromosomes in the GnomAD database, including 277 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.019 ( 46 hom., cov: 32)
Exomes 𝑓: 0.027 ( 231 hom. )
Consequence
SLC26A4
NM_000441.2 intron
NM_000441.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.423
Genes affected
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 7-107661378-C-T is Benign according to our data. Variant chr7-107661378-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1217919.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0187 (2854/152350) while in subpopulation NFE AF= 0.027 (1839/68018). AF 95% confidence interval is 0.026. There are 46 homozygotes in gnomad4. There are 1328 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 46 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A4 | NM_000441.2 | c.-3-261C>T | intron_variant | ENST00000644269.2 | |||
SLC26A4-AS1 | NR_028137.1 | n.197+224G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A4 | ENST00000644269.2 | c.-3-261C>T | intron_variant | NM_000441.2 | P1 | ||||
SLC26A4-AS1 | ENST00000668981.1 | n.257+224G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2856AN: 152232Hom.: 46 Cov.: 32
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GnomAD4 exome AF: 0.0266 AC: 11388AN: 427634Hom.: 231 Cov.: 2 AF XY: 0.0278 AC XY: 6263AN XY: 225504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 24, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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