rs6741892
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_138801.3(GALM):c.568A>T(p.Asn190Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0981 in 1,601,982 control chromosomes in the GnomAD database, including 9,958 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_138801.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALM | NM_138801.3 | c.568A>T | p.Asn190Tyr | missense_variant | Exon 4 of 7 | ENST00000272252.10 | NP_620156.1 | |
GALM | XM_011532540.3 | c.568A>T | p.Asn190Tyr | missense_variant | Exon 4 of 6 | XP_011530842.1 | ||
GALM | XM_047443419.1 | c.568A>T | p.Asn190Tyr | missense_variant | Exon 4 of 6 | XP_047299375.1 | ||
LOC124905993 | XR_007086292.1 | n.220-4154T>A | intron_variant | Intron 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALM | ENST00000272252.10 | c.568A>T | p.Asn190Tyr | missense_variant | Exon 4 of 7 | 1 | NM_138801.3 | ENSP00000272252.5 | ||
GALM | ENST00000434934.1 | c.208A>T | p.Asn70Tyr | missense_variant | Exon 2 of 5 | 3 | ENSP00000399473.1 | |||
GALM | ENST00000410063.5 | c.190+23477A>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000386233.1 | ||||
GALM | ENST00000444351.5 | n.487A>T | non_coding_transcript_exon_variant | Exon 4 of 7 | 5 | ENSP00000409083.1 |
Frequencies
GnomAD3 genomes AF: 0.133 AC: 20280AN: 152070Hom.: 1746 Cov.: 32
GnomAD3 exomes AF: 0.123 AC: 30385AN: 246072Hom.: 2387 AF XY: 0.123 AC XY: 16404AN XY: 133262
GnomAD4 exome AF: 0.0944 AC: 136875AN: 1449794Hom.: 8198 Cov.: 28 AF XY: 0.0973 AC XY: 70248AN XY: 721822
GnomAD4 genome AF: 0.134 AC: 20330AN: 152188Hom.: 1760 Cov.: 32 AF XY: 0.136 AC XY: 10094AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 02, 2025 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Galactosemia 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
GALM-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 18, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at