chr2-96649662-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001293083.2(FER1L5):c.379G>T(p.Asp127Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,551,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001293083.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER1L5 | NM_001293083.2 | c.379G>T | p.Asp127Tyr | missense_variant | 5/53 | ENST00000624922.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER1L5 | ENST00000624922.6 | c.379G>T | p.Asp127Tyr | missense_variant | 5/53 | 5 | NM_001293083.2 | P4 | |
FER1L5 | ENST00000623019.5 | c.379G>T | p.Asp127Tyr | missense_variant | 5/52 | A2 | |||
FER1L5 | ENST00000505256.6 | n.387G>T | non_coding_transcript_exon_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000447 AC: 7AN: 156500Hom.: 0 AF XY: 0.0000482 AC XY: 4AN XY: 82944
GnomAD4 exome AF: 0.00000500 AC: 7AN: 1399264Hom.: 0 Cov.: 31 AF XY: 0.00000580 AC XY: 4AN XY: 690146
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.379G>T (p.D127Y) alteration is located in exon 5 (coding exon 5) of the FER1L5 gene. This alteration results from a G to T substitution at nucleotide position 379, causing the aspartic acid (D) at amino acid position 127 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at