rs57739618
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001853.4(COL9A3):c.685-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000244 in 1,559,398 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001853.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL9A3 | ENST00000649368.1 | c.685-4G>A | splice_region_variant, intron_variant | NM_001853.4 | ENSP00000496793.1 | |||||
COL9A3 | ENST00000463487.2 | n.393-4G>A | splice_region_variant, intron_variant | 5 | ||||||
COL9A3 | ENST00000489045.5 | n.731-4G>A | splice_region_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000658 AC: 11AN: 167238Hom.: 1 AF XY: 0.000101 AC XY: 9AN XY: 89276
GnomAD4 exome AF: 0.0000192 AC: 27AN: 1407298Hom.: 1 Cov.: 33 AF XY: 0.0000259 AC XY: 18AN XY: 695360
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74294
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at