rs781861717
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PP2PP3_ModerateBP6_ModerateBS2
The NM_001110556.2(FLNA):c.3647C>T(p.Thr1216Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,208,529 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T1216T) has been classified as Likely benign.
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.3647C>T | p.Thr1216Met | missense_variant | 22/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.3647C>T | p.Thr1216Met | missense_variant | 22/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.3647C>T | p.Thr1216Met | missense_variant | 22/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000883 AC: 1AN: 113286Hom.: 0 Cov.: 25 AF XY: 0.0000282 AC XY: 1AN XY: 35428
GnomAD3 exomes AF: 0.0000167 AC: 3AN: 179779Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 66919
GnomAD4 exome AF: 0.00000730 AC: 8AN: 1095243Hom.: 0 Cov.: 33 AF XY: 0.00000830 AC XY: 3AN XY: 361431
GnomAD4 genome ? AF: 0.00000883 AC: 1AN: 113286Hom.: 0 Cov.: 25 AF XY: 0.0000282 AC XY: 1AN XY: 35428
ClinVar
Submissions by phenotype
Melnick-Needles syndrome;C0265293:Frontometaphyseal dysplasia;C1844696:Oto-palato-digital syndrome, type II;C1848213:Heterotopia, periventricular, X-linked dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at