chr9-133332570-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006753.6(SURF6):c.584C>T(p.Pro195Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000392 in 1,608,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006753.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SURF6 | NM_006753.6 | c.584C>T | p.Pro195Leu | missense_variant | 4/5 | ENST00000372022.6 | NP_006744.2 | |
SURF6 | NM_001278942.2 | c.583C>T | p.Arg195Cys | missense_variant | 4/5 | NP_001265871.1 | ||
SURF6 | NR_103874.2 | n.587C>T | non_coding_transcript_exon_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SURF6 | ENST00000372022.6 | c.584C>T | p.Pro195Leu | missense_variant | 4/5 | 1 | NM_006753.6 | ENSP00000361092 | P1 | |
SURF6 | ENST00000468290.1 | n.370C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000285 AC: 7AN: 245466Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133412
GnomAD4 exome AF: 0.0000343 AC: 50AN: 1456424Hom.: 0 Cov.: 32 AF XY: 0.0000359 AC XY: 26AN XY: 724810
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2024 | The c.584C>T (p.P195L) alteration is located in exon 4 (coding exon 4) of the SURF6 gene. This alteration results from a C to T substitution at nucleotide position 584, causing the proline (P) at amino acid position 195 to be replaced by a leucine (L). 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