2-38675812-G-T

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.882
Variant links:
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
GALMNM_138801.3 linkc.191-100G>T intron_variant ENST00000272252.10 NP_620156.1 Q96C23A0A384MDW6
GALMXM_011532540.3 linkc.191-100G>T intron_variant XP_011530842.1 Q96C23
GALMXM_047443419.1 linkc.191-100G>T intron_variant XP_047299375.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GALMENST00000272252.10 linkc.191-100G>T intron_variant 1 NM_138801.3 ENSP00000272252.5 Q96C23
GALMENST00000410063.5 linkc.190+9461G>T intron_variant 3 ENSP00000386233.1 B8ZZ75
GALMENST00000427858.4 linkn.272-100G>T intron_variant 4
GALMENST00000444351.5 linkn.110-100G>T intron_variant 5 ENSP00000409083.1 H7C320

Frequencies

GnomAD3 genomes
AF:
0.0134
AC:
2041
AN:
151762
Hom.:
49
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0468
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00421
Gnomad ASJ
AF:
0.00347
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.00819
GnomAD4 exome
AF:
0.00161
AC:
1478
AN:
917590
Hom.:
28
AF XY:
0.00134
AC XY:
634
AN XY:
472526
show subpopulations
Gnomad4 AFR exome
AF:
0.0467
Gnomad4 AMR exome
AF:
0.00240
Gnomad4 ASJ exome
AF:
0.00341
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000432
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000139
Gnomad4 OTH exome
AF:
0.00353
GnomAD4 genome
AF:
0.0135
AC:
2048
AN:
151880
Hom.:
49
Cov.:
30
AF XY:
0.0133
AC XY:
986
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.0468
Gnomad4 AMR
AF:
0.00421
Gnomad4 ASJ
AF:
0.00347
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.00810
Alfa
AF:
0.000775
Hom.:
0
Bravo
AF:
0.0154
Asia WGS
AF:
0.00144
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 25, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.37
DANN
Benign
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149949698; hg19: chr2-38902954; API