rs4979085
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022486.5(SUSD1):c.103+6307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_022486.5 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUSD1 | ENST00000374270.8 | c.103+6307C>T | intron_variant | Intron 1 of 16 | 1 | NM_022486.5 | ENSP00000363388.4 | |||
SUSD1 | ENST00000374264.6 | c.103+6307C>T | intron_variant | Intron 1 of 17 | 1 | ENSP00000363382.2 | ||||
SUSD1 | ENST00000374263.7 | c.103+6307C>T | intron_variant | Intron 1 of 15 | 2 | ENSP00000363381.3 | ||||
SUSD1 | ENST00000355396.7 | c.52+6307C>T | intron_variant | Intron 1 of 15 | 2 | ENSP00000347558.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151932Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151932Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74182 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at