chr9-133353914-T-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_003172.4(SURF1):c.350A>T(p.Tyr117Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y117S) has been classified as Uncertain significance.
Frequency
Consequence
NM_003172.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SURF1 | NM_003172.4 | c.350A>T | p.Tyr117Phe | missense_variant | 5/9 | ENST00000371974.8 | |
SURF1 | NM_001280787.1 | c.23A>T | p.Tyr8Phe | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SURF1 | ENST00000371974.8 | c.350A>T | p.Tyr117Phe | missense_variant | 5/9 | 1 | NM_003172.4 | P1 | |
SURF1 | ENST00000615505.4 | c.23A>T | p.Tyr8Phe | missense_variant | 4/8 | 1 | |||
SURF1 | ENST00000437995.1 | n.296A>T | non_coding_transcript_exon_variant | 4/8 | 5 | ||||
SURF1 | ENST00000495952.5 | n.340A>T | non_coding_transcript_exon_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at