chr22-23868556-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_001024939.4(SLC2A11):c.205A>G(p.Met69Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000996 in 1,614,052 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001024939.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A11 | NM_001024939.4 | c.205A>G | p.Met69Val | missense_variant | 3/12 | ENST00000316185.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A11 | ENST00000316185.9 | c.205A>G | p.Met69Val | missense_variant | 3/12 | 1 | NM_001024939.4 | ||
ENST00000624923.1 | n.4722T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000254 AC: 64AN: 251492Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135922
GnomAD4 exome AF: 0.00108 AC: 1572AN: 1461892Hom.: 2 Cov.: 30 AF XY: 0.00108 AC XY: 787AN XY: 727246
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at