3-74285307-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020872.3(CNTN3):c.2702C>T(p.Thr901Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0096 in 1,601,278 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict 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_020872.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN3 | NM_020872.3 | c.2702C>T | p.Thr901Met | missense_variant, splice_region_variant | 20/23 | ENST00000263665.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN3 | ENST00000263665.7 | c.2702C>T | p.Thr901Met | missense_variant, splice_region_variant | 20/23 | 1 | NM_020872.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00806 AC: 1225AN: 151986Hom.: 8 Cov.: 31
GnomAD3 exomes AF: 0.00823 AC: 1956AN: 237704Hom.: 19 AF XY: 0.00820 AC XY: 1060AN XY: 129228
GnomAD4 exome AF: 0.00976 AC: 14150AN: 1449174Hom.: 81 Cov.: 30 AF XY: 0.00955 AC XY: 6888AN XY: 721480
GnomAD4 genome AF: 0.00805 AC: 1224AN: 152104Hom.: 8 Cov.: 31 AF XY: 0.00792 AC XY: 589AN XY: 74344
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at