chr3-40044269-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The ENST00000396217.7(MYRIP):c.200G>A(p.Arg67Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,613,990 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict 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 Benign (★).
Frequency
Consequence
ENST00000396217.7 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYRIP | NM_015460.4 | c.330G>A | p.Ala110= | splice_region_variant, synonymous_variant | 3/17 | ENST00000302541.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYRIP | ENST00000302541.11 | c.330G>A | p.Ala110= | splice_region_variant, synonymous_variant | 3/17 | 1 | NM_015460.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00168 AC: 256AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00216 AC: 539AN: 249996Hom.: 0 AF XY: 0.00243 AC XY: 329AN XY: 135202
GnomAD4 exome AF: 0.00246 AC: 3593AN: 1461662Hom.: 9 Cov.: 31 AF XY: 0.00248 AC XY: 1806AN XY: 727156
GnomAD4 genome ? AF: 0.00169 AC: 257AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.00168 AC XY: 125AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at