rs4664114
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_052905.4(FMNL2):āc.120T>Cā(p.Asn40=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 1,608,258 control chromosomes in the GnomAD database, including 370,392 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_052905.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMNL2 | NM_052905.4 | c.120T>C | p.Asn40= | splice_region_variant, synonymous_variant | 2/26 | ENST00000288670.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMNL2 | ENST00000288670.14 | c.120T>C | p.Asn40= | splice_region_variant, synonymous_variant | 2/26 | 1 | NM_052905.4 | P1 | |
FMNL2 | ENST00000475377.3 | c.120T>C | p.Asn40= | splice_region_variant, synonymous_variant | 2/28 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.676 AC: 102587AN: 151862Hom.: 34836 Cov.: 31
GnomAD3 exomes AF: 0.694 AC: 171716AN: 247598Hom.: 60166 AF XY: 0.687 AC XY: 92238AN XY: 134280
GnomAD4 exome AF: 0.677 AC: 986407AN: 1456278Hom.: 335535 Cov.: 33 AF XY: 0.676 AC XY: 490171AN XY: 724644
GnomAD4 genome ? AF: 0.675 AC: 102648AN: 151980Hom.: 34857 Cov.: 31 AF XY: 0.678 AC XY: 50317AN XY: 74242
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at