2-38675812-G-T
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_138801.3(GALM):c.191-100G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 1,069,470 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.013 ( 49 hom., cov: 30)
Exomes 𝑓: 0.0016 ( 28 hom. )
Consequence
GALM
NM_138801.3 intron
NM_138801.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.882
Genes affected
GALM (HGNC:24063): (galactose mutarotase) This gene encodes an enzyme that catalyzes the epimerization of hexose sugars such as glucose and galactose. The encoded protein is expressed in the cytoplasm and has a preference for galactose. The encoded protein may be required for normal galactose metabolism by maintaining the equilibrium of alpha and beta anomers of galactose.[provided by RefSeq, Mar 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 2-38675812-G-T is Benign according to our data. Variant chr2-38675812-G-T is described in ClinVar as [Benign]. Clinvar id is 1295014.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0135 (2048/151880) while in subpopulation AFR AF= 0.0468 (1937/41390). AF 95% confidence interval is 0.0451. There are 49 homozygotes in gnomad4. There are 986 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 49 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALM | NM_138801.3 | c.191-100G>T | intron_variant | ENST00000272252.10 | NP_620156.1 | |||
GALM | XM_011532540.3 | c.191-100G>T | intron_variant | XP_011530842.1 | ||||
GALM | XM_047443419.1 | c.191-100G>T | intron_variant | XP_047299375.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALM | ENST00000272252.10 | c.191-100G>T | intron_variant | 1 | NM_138801.3 | ENSP00000272252.5 | ||||
GALM | ENST00000410063.5 | c.190+9461G>T | intron_variant | 3 | ENSP00000386233.1 | |||||
GALM | ENST00000427858.4 | n.272-100G>T | intron_variant | 4 | ||||||
GALM | ENST00000444351.5 | n.110-100G>T | intron_variant | 5 | ENSP00000409083.1 |
Frequencies
GnomAD3 genomes AF: 0.0134 AC: 2041AN: 151762Hom.: 49 Cov.: 30
GnomAD3 genomes
AF:
AC:
2041
AN:
151762
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00161 AC: 1478AN: 917590Hom.: 28 AF XY: 0.00134 AC XY: 634AN XY: 472526
GnomAD4 exome
AF:
AC:
1478
AN:
917590
Hom.:
AF XY:
AC XY:
634
AN XY:
472526
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0135 AC: 2048AN: 151880Hom.: 49 Cov.: 30 AF XY: 0.0133 AC XY: 986AN XY: 74260
GnomAD4 genome
AF:
AC:
2048
AN:
151880
Hom.:
Cov.:
30
AF XY:
AC XY:
986
AN XY:
74260
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
5
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 25, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at