rs587781184
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_003172.4(SURF1):c.54+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.004 in 1,390,498 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003172.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SURF1 | ENST00000371974.8 | c.54+10G>A | intron_variant | Intron 1 of 8 | 1 | NM_003172.4 | ENSP00000361042.3 | |||
SURF1 | ENST00000615505.4 | c.-222+10G>A | intron_variant | Intron 1 of 7 | 1 | ENSP00000482067.1 | ||||
SURF1 | ENST00000463965.1 | n.277+10G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00285 AC: 433AN: 151754Hom.: 5 Cov.: 34
GnomAD3 exomes AF: 0.00535 AC: 127AN: 23718Hom.: 2 AF XY: 0.00554 AC XY: 80AN XY: 14446
GnomAD4 exome AF: 0.00414 AC: 5127AN: 1238638Hom.: 14 Cov.: 36 AF XY: 0.00411 AC XY: 2493AN XY: 607026
GnomAD4 genome AF: 0.00285 AC: 433AN: 151860Hom.: 5 Cov.: 34 AF XY: 0.00277 AC XY: 206AN XY: 74242
ClinVar
Submissions by phenotype
not provided Benign:3
SURF1: BS2 -
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Leigh syndrome Uncertain:1Benign:1
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at