6-41778251-A-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006653.5(FRS3):c.-167-75T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FRS3
NM_006653.5 intron
NM_006653.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.427
Genes affected
FRS3 (HGNC:16970): (fibroblast growth factor receptor substrate 3) This gene encodes a substrate for the fibroblast growth factor receptor. The encoded protein is found in the peripheral plasma membrane and links fibroblast growth factor receptor stimulation to activators of Ras. The encoded protein down-regulates extracellular regulated kinase 2 through direct binding. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRS3 | NM_006653.5 | c.-167-75T>A | intron_variant | ENST00000373018.7 | NP_006644.1 | |||
FRS3 | XM_011514254.2 | c.-167-75T>A | intron_variant | XP_011512556.1 | ||||
FRS3 | XM_047418097.1 | c.-167-75T>A | intron_variant | XP_047274053.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRS3 | ENST00000373018.7 | c.-167-75T>A | intron_variant | 3 | NM_006653.5 | ENSP00000362109 | P1 | |||
FRS3 | ENST00000422888.5 | c.-167-75T>A | intron_variant | 5 | ENSP00000413214 | |||||
FRS3 | ENST00000426290.1 | c.50-1241T>A | intron_variant | 3 | ENSP00000396715 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 104Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
104
Hom.:
AF XY:
AC XY:
0
AN XY:
64
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at