rs1382347293
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001999.4(FBN2):c.5918-4A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,612,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001999.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBN2 | NM_001999.4 | c.5918-4A>G | splice_region_variant, intron_variant | ENST00000262464.9 | NP_001990.2 | |||
FBN2 | XM_017009228.3 | c.5765-4A>G | splice_region_variant, intron_variant | XP_016864717.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBN2 | ENST00000262464.9 | c.5918-4A>G | splice_region_variant, intron_variant | 1 | NM_001999.4 | ENSP00000262464.4 | ||||
FBN2 | ENST00000703783.1 | n.2702-4A>G | splice_region_variant, intron_variant | |||||||
FBN2 | ENST00000703785.1 | n.2621-4A>G | splice_region_variant, intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250560Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135448
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460564Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726624
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
Congenital contractural arachnodactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 12, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at