chr14-60645386-CAAACTAG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005982.4(SIX1):c.*890_*896del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 152,110 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Consequence
SIX1
NM_005982.4 3_prime_UTR
NM_005982.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.57
Genes affected
SIX1 (HGNC:10887): (SIX homeobox 1) The protein encoded by this gene is a homeobox protein that is similar to the Drosophila 'sine oculis' gene product. This gene is found in a cluster of related genes on chromosome 14 and is thought to be involved in limb development. Defects in this gene are a cause of autosomal dominant deafness type 23 (DFNA23) and branchiootic syndrome type 3 (BOS3). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 14-60645386-CAAACTAG-C is Benign according to our data. Variant chr14-60645386-CAAACTAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 313448.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000145 (22/152110) while in subpopulation AMR AF= 0.00105 (16/15288). AF 95% confidence interval is 0.000656. There are 0 homozygotes in gnomad4. There are 17 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 22 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIX1 | NM_005982.4 | c.*890_*896del | 3_prime_UTR_variant | 2/2 | ENST00000645694.3 | ||
SIX1 | XM_017021602.3 | c.*1164_*1170del | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIX1 | ENST00000645694.3 | c.*890_*896del | 3_prime_UTR_variant | 2/2 | NM_005982.4 | P1 | |||
SIX1 | ENST00000554986.2 | c.*890_*896del | 3_prime_UTR_variant | 2/2 | 3 | ||||
SIX1 | ENST00000553535.2 | n.1433_1439del | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
SIX1 | ENST00000555955.3 | n.2382_2388del | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 151994Hom.: 0 Cov.: 32
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GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74372
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Nonsyndromic Hearing Loss, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Branchiootorenal Spectrum Disorders Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at