rs781934508
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003172.4(SURF1):c.751+5G>T variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.00000137 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003172.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SURF1 | NM_003172.4 | c.751+5G>T | splice_donor_5th_base_variant, intron_variant | ENST00000371974.8 | |||
SURF1 | NM_001280787.1 | c.424+5G>T | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SURF1 | ENST00000371974.8 | c.751+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_003172.4 | P1 | |||
SURF1 | ENST00000615505.4 | c.424+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | |||||
SURF1 | ENST00000437995.1 | n.661+5G>T | splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant | 5 | |||||
SURF1 | ENST00000495952.5 | n.741+5G>T | splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727236
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at