chr11-101944258-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_020802.4(CEP126):c.249-7A>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,560,540 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_020802.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP126 | NM_020802.4 | c.249-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000263468.13 | |||
CEP126 | NM_001363543.2 | c.-1031-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP126 | ENST00000263468.13 | c.249-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020802.4 | P1 | |||
CEP126 | ENST00000670091.1 | c.249-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | ||||||
CEP126 | ENST00000670318.1 | c.249-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00579 AC: 880AN: 152054Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00139 AC: 286AN: 205514Hom.: 3 AF XY: 0.000980 AC XY: 110AN XY: 112274
GnomAD4 exome AF: 0.000540 AC: 760AN: 1408368Hom.: 6 Cov.: 30 AF XY: 0.000452 AC XY: 316AN XY: 699108
GnomAD4 genome AF: 0.00586 AC: 892AN: 152172Hom.: 11 Cov.: 32 AF XY: 0.00598 AC XY: 445AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 16, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at