2-38666535-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_138801.3(GALM):​c.190+184G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,972 control chromosomes in the GnomAD database, including 6,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 6351 hom., cov: 32)

Consequence

GALM
NM_138801.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.819
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 2-38666535-G-A is Benign according to our data. Variant chr2-38666535-G-A is described in ClinVar as [Benign]. Clinvar id is 1290378.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GALMNM_138801.3 linkc.190+184G>A intron_variant ENST00000272252.10 NP_620156.1 Q96C23A0A384MDW6
GALMXM_011532540.3 linkc.190+184G>A intron_variant XP_011530842.1 Q96C23
GALMXM_047443419.1 linkc.190+184G>A intron_variant XP_047299375.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GALMENST00000272252.10 linkc.190+184G>A intron_variant 1 NM_138801.3 ENSP00000272252.5 Q96C23
GALMENST00000410063.5 linkc.190+184G>A intron_variant 3 ENSP00000386233.1 B8ZZ75
GALMENST00000427858.4 linkn.271+184G>A intron_variant 4
GALMENST00000444351.5 linkn.109+184G>A intron_variant 5 ENSP00000409083.1 H7C320

Frequencies

GnomAD3 genomes
AF:
0.238
AC:
36137
AN:
151854
Hom.:
6340
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.491
Gnomad AMI
AF:
0.134
Gnomad AMR
AF:
0.173
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.389
Gnomad SAS
AF:
0.229
Gnomad FIN
AF:
0.0899
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.119
Gnomad OTH
AF:
0.203
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.238
AC:
36185
AN:
151972
Hom.:
6351
Cov.:
32
AF XY:
0.237
AC XY:
17628
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.491
Gnomad4 AMR
AF:
0.173
Gnomad4 ASJ
AF:
0.151
Gnomad4 EAS
AF:
0.389
Gnomad4 SAS
AF:
0.229
Gnomad4 FIN
AF:
0.0899
Gnomad4 NFE
AF:
0.119
Gnomad4 OTH
AF:
0.200
Alfa
AF:
0.181
Hom.:
496
Bravo
AF:
0.255
Asia WGS
AF:
0.317
AC:
1103
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 12, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.66
DANN
Benign
0.77

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: rs7590750; hg19: chr2-38893677; API