rs199803218
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP3BP6_ModerateBS1BS2
The NM_001110556.2(FLNA):c.4755+5G>A variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.0000529 in 1,208,782 control chromosomes in the GnomAD database, including 4 homozygotes. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001110556.2 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.4755+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000369850.10 | |||
FLNA | NM_001456.4 | c.4755+5G>A | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.4755+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000889 AC: 1AN: 112478Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34622
GnomAD3 exomes AF: 0.0000567 AC: 10AN: 176504Hom.: 0 AF XY: 0.0000308 AC XY: 2AN XY: 64898
GnomAD4 exome AF: 0.0000575 AC: 63AN: 1096251Hom.: 4 Cov.: 32 AF XY: 0.0000331 AC XY: 12AN XY: 362513
GnomAD4 genome ? AF: 0.00000889 AC: 1AN: 112531Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34685
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 | Jan 25, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at