chr1-75238549-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130058.2(SLC44A5):c.620G>T(p.Gly207Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,448,946 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 Uncertain significance (★).
Frequency
Consequence
NM_001130058.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC44A5 | NM_001130058.2 | c.620G>T | p.Gly207Val | missense_variant | 10/24 | ENST00000370859.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A5 | ENST00000370859.8 | c.620G>T | p.Gly207Val | missense_variant | 10/24 | 2 | NM_001130058.2 | A1 | |
SLC44A5 | ENST00000370855.5 | c.620G>T | p.Gly207Val | missense_variant | 10/24 | 1 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000827 AC: 2AN: 241958Hom.: 0 AF XY: 0.00000763 AC XY: 1AN XY: 131062
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1448946Hom.: 0 Cov.: 29 AF XY: 0.00000832 AC XY: 6AN XY: 720826
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.620G>T (p.G207V) alteration is located in exon 10 (coding exon 9) of the SLC44A5 gene. This alteration results from a G to T substitution at nucleotide position 620, causing the glycine (G) at amino acid position 207 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at