chr4-122876325-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001361665.2(FGF2):c.183G>T(p.Lys61Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000387 in 1,605,748 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001361665.2 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
FGF2 | NM_001361665.2 | c.183G>T | p.Lys61Asn | missense_variant | 2/3 | ENST00000644866.2 | |
FGF2 | NM_002006.6 | c.582G>T | p.Lys194Asn | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF2 | ENST00000644866.2 | c.183G>T | p.Lys61Asn | missense_variant | 2/3 | NM_001361665.2 | P1 | ||
FGF2 | ENST00000264498.9 | c.582G>T | p.Lys194Asn | missense_variant | 2/3 | 1 | |||
FGF2 | ENST00000608478.1 | c.183G>T | p.Lys61Asn | missense_variant | 2/3 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00163 AC: 248AN: 151930Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000593 AC: 149AN: 251428Hom.: 1 AF XY: 0.000442 AC XY: 60AN XY: 135888
GnomAD4 exome AF: 0.000257 AC: 374AN: 1453700Hom.: 3 Cov.: 29 AF XY: 0.000229 AC XY: 166AN XY: 723806
GnomAD4 genome ? AF: 0.00163 AC: 248AN: 152048Hom.: 1 Cov.: 32 AF XY: 0.00166 AC XY: 123AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at