chr5-108897661-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005246.4(FER):c.1049T>C(p.Ile350Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000969 in 1,586,526 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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 (★).
Frequency
Consequence
NM_005246.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
FER | NM_005246.4 | c.1049T>C | p.Ile350Thr | missense_variant, splice_region_variant | 10/20 | ENST00000281092.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER | ENST00000281092.9 | c.1049T>C | p.Ile350Thr | missense_variant, splice_region_variant | 10/20 | 1 | NM_005246.4 | P1 | |
FER | ENST00000438717.6 | c.-185T>C | 5_prime_UTR_variant | 1/11 | 2 | ||||
FER | ENST00000504143.6 | c.*520T>C | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 8/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00524 AC: 797AN: 152200Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00132 AC: 300AN: 226956Hom.: 4 AF XY: 0.000998 AC XY: 123AN XY: 123260
GnomAD4 exome AF: 0.000516 AC: 740AN: 1434208Hom.: 5 Cov.: 30 AF XY: 0.000456 AC XY: 325AN XY: 712924
GnomAD4 genome ? AF: 0.00524 AC: 798AN: 152318Hom.: 8 Cov.: 32 AF XY: 0.00525 AC XY: 391AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at