1-75227815-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001130058.2(SLC44A5):c.896G>A(p.Arg299His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,599,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001130058.2 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 |
---|---|---|---|---|---|---|---|
SLC44A5 | NM_001130058.2 | c.896G>A | p.Arg299His | missense_variant | 13/24 | ENST00000370859.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A5 | ENST00000370859.8 | c.896G>A | p.Arg299His | missense_variant | 13/24 | 2 | NM_001130058.2 | A1 | |
SLC44A5 | ENST00000370855.5 | c.896G>A | p.Arg299His | missense_variant | 13/24 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000844 AC: 2AN: 236930Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128380
GnomAD4 exome AF: 0.0000111 AC: 16AN: 1447296Hom.: 0 Cov.: 29 AF XY: 0.0000139 AC XY: 10AN XY: 719828
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74262
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 26, 2023 | 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