14-37826179-TGGAAAATTATTTTAGGCCCAA-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PVS1_ModerateBP6_ModerateBS2
The NM_001310135.5(TTC6):c.4975-7_4988del variant causes a splice acceptor, coding sequence, intron change. The variant allele was found at a frequency of 0.00517 in 1,586,596 control chromosomes in the GnomAD database, including 33 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0035 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0053 ( 28 hom. )
Consequence
TTC6
NM_001310135.5 splice_acceptor, coding_sequence, intron
NM_001310135.5 splice_acceptor, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.94
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.02685038 fraction of the gene. Cryptic splice site detected, with MaxEntScore 6.8, offset of 28, new splice context is: ccactttaccattgccatAGata. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
BP6
Variant 14-37826179-TGGAAAATTATTTTAGGCCCAA-T is Benign according to our data. Variant chr14-37826179-TGGAAAATTATTTTAGGCCCAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644187.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC6 | NM_001310135.5 | c.4975-7_4988del | splice_acceptor_variant, coding_sequence_variant, intron_variant | 30/33 | ENST00000553443.6 | NP_001297064.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTC6 | ENST00000553443.6 | c.4975-7_4988del | splice_acceptor_variant, coding_sequence_variant, intron_variant | 30/33 | 5 | NM_001310135.5 | ENSP00000451131 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00352 AC: 535AN: 152058Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00363 AC: 819AN: 225896Hom.: 4 AF XY: 0.00368 AC XY: 451AN XY: 122636
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GnomAD4 exome AF: 0.00534 AC: 7662AN: 1434420Hom.: 28 AF XY: 0.00521 AC XY: 3713AN XY: 713270
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GnomAD4 genome AF: 0.00352 AC: 535AN: 152176Hom.: 5 Cov.: 32 AF XY: 0.00313 AC XY: 233AN XY: 74410
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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 | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | TTC6: BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at