chr1-117075222-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003594.4(TTF2):āc.638A>Gā(p.Lys213Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00345 in 1,614,220 control chromosomes in the GnomAD database, including 156 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 ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003594.4 missense
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 |
---|---|---|---|---|---|---|---|
TTF2 | NM_003594.4 | c.638A>G | p.Lys213Arg | missense_variant | 5/23 | ENST00000369466.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTF2 | ENST00000369466.9 | c.638A>G | p.Lys213Arg | missense_variant | 5/23 | 1 | NM_003594.4 | P1 | |
TTF2 | ENST00000470935.1 | n.627A>G | non_coding_transcript_exon_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0179 AC: 2719AN: 152210Hom.: 79 Cov.: 32
GnomAD3 exomes AF: 0.00483 AC: 1213AN: 251148Hom.: 39 AF XY: 0.00345 AC XY: 469AN XY: 135880
GnomAD4 exome AF: 0.00194 AC: 2835AN: 1461892Hom.: 77 Cov.: 78 AF XY: 0.00165 AC XY: 1197AN XY: 727246
GnomAD4 genome AF: 0.0179 AC: 2730AN: 152328Hom.: 79 Cov.: 32 AF XY: 0.0170 AC XY: 1269AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at