6-167181844-G-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The XR_001743415.1(TCP10L2):n.1187G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 12)
Exomes 𝑓: 0.000095 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TCP10L2
XR_001743415.1 non_coding_transcript_exon
XR_001743415.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.138
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 6-167181844-G-A is Benign according to our data. Variant chr6-167181844-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657128.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCP10L2 | XR_001743415.1 | n.1187G>A | non_coding_transcript_exon_variant | Exon 8 of 10 | ||||
TCP10L2 | XR_007059868.1 | n.1095G>A | non_coding_transcript_exon_variant | Exon 8 of 10 | ||||
TCP10L2 | XR_007059869.1 | n.1095G>A | non_coding_transcript_exon_variant | Exon 8 of 11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCP10L2 | ENST00000697192.1 | n.870+1111G>A | intron_variant | Intron 6 of 9 |
Frequencies
GnomAD3 genomes AF: 0.0000327 AC: 3AN: 91696Hom.: 0 Cov.: 12
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GnomAD3 exomes AF: 0.0000248 AC: 6AN: 242294Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 131928
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000950 AC: 136AN: 1431976Hom.: 0 Cov.: 30 AF XY: 0.0000941 AC XY: 67AN XY: 711652
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000327 AC: 3AN: 91696Hom.: 0 Cov.: 12 AF XY: 0.0000228 AC XY: 1AN XY: 43870
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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
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
TCP10L2: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at