chr6-63720623-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001142800.2(EYS):c.9408T>C(p.Asp3136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000074 in 1,351,156 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 (★).
Frequency
Consequence
NM_001142800.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.9408T>C | p.Asp3136= | synonymous_variant | 43/43 | ENST00000503581.6 | |
PHF3 | NM_001370348.2 | c.*6915A>G | 3_prime_UTR_variant | 16/16 | ENST00000262043.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.9408T>C | p.Asp3136= | synonymous_variant | 43/43 | 5 | NM_001142800.2 | A2 | |
EYS | ENST00000370621.7 | c.9471T>C | p.Asp3157= | synonymous_variant | 44/44 | 1 | P2 | ||
PHF3 | ENST00000262043.8 | c.*6915A>G | 3_prime_UTR_variant | 16/16 | 5 | NM_001370348.2 | P1 | ||
PHF3 | ENST00000505138.1 | c.363+9261A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.40e-7 AC: 1AN: 1351156Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 662894
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.