1-94540363-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001993.5(F3):āc.106A>Gā(p.Thr36Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00129 in 1,610,278 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001993.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
F3 | NM_001993.5 | c.106A>G | p.Thr36Ala | missense_variant | 2/6 | ENST00000334047.12 | NP_001984.1 | |
F3 | NM_001178096.2 | c.106A>G | p.Thr36Ala | missense_variant | 2/5 | NP_001171567.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F3 | ENST00000334047.12 | c.106A>G | p.Thr36Ala | missense_variant | 2/6 | 1 | NM_001993.5 | ENSP00000334145.7 | ||
F3 | ENST00000370207.4 | c.106A>G | p.Thr36Ala | missense_variant | 2/5 | 1 | ENSP00000359226.4 | |||
F3 | ENST00000480356.1 | n.724A>G | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00700 AC: 1066AN: 152238Hom.: 13 Cov.: 33
GnomAD3 exomes AF: 0.00180 AC: 452AN: 250872Hom.: 7 AF XY: 0.00130 AC XY: 176AN XY: 135652
GnomAD4 exome AF: 0.000690 AC: 1006AN: 1457922Hom.: 12 Cov.: 28 AF XY: 0.000600 AC XY: 435AN XY: 725588
GnomAD4 genome AF: 0.00701 AC: 1068AN: 152356Hom.: 13 Cov.: 33 AF XY: 0.00664 AC XY: 495AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at