rs28715079
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_003172.4(SURF1):c.573C>T(p.Thr191Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T191T) has been classified as Likely benign.
Frequency
Consequence
NM_003172.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- Leigh syndromeInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
- mitochondrial complex IV deficiency, nuclear type 1Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
- Charcot-Marie-Tooth disease type 4KInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
- Leigh syndrome with cardiomyopathyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Leigh syndrome with leukodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SURF1 | ENST00000371974.8 | c.573C>T | p.Thr191Thr | synonymous_variant | Exon 6 of 9 | 1 | NM_003172.4 | ENSP00000361042.3 | ||
SURF1 | ENST00000615505.4 | c.246C>T | p.Thr82Thr | synonymous_variant | Exon 5 of 8 | 1 | ENSP00000482067.1 | |||
SURF1 | ENST00000437995.1 | n.483C>T | non_coding_transcript_exon_variant | Exon 5 of 8 | 5 | |||||
SURF1 | ENST00000495952.5 | n.563C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000561 AC: 14AN: 249408 AF XY: 0.0000370 show subpopulations
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460982Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 6AN XY: 726738 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74350 show subpopulations
ClinVar
Submissions by phenotype
Leigh syndrome Benign:1
- -
SURF1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at