2-38682564-G-T

Position:

• chr2-38682564-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138801.3(GALM):​c.552+1078G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,094 control chromosomes in the GnomAD database, including 886 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (886 hom., cov: 32)
• Consequence: GALM NM_138801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALM	NM_138801.3	c.552+1078G>T		intron_variant		ENST00000272252.10
GALM	XM_011532540.3	c.552+1078G>T		intron_variant
GALM	XM_047443419.1	c.552+1078G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALM	ENST00000272252.10	c.552+1078G>T		intron_variant		1	NM_138801.3	P1
GALM	ENST00000410063.5	c.190+16213G>T		intron_variant		3
GALM	ENST00000434934.1	c.192+1078G>T		intron_variant		3
GALM	ENST00000444351.5	c.471+1078G>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15346 AN: 151976 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0905

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.101 AC: 15378 AN: 152094 Hom.: 886 Cov.: 32 AF XY: 0.105 AC XY: 7775 AN XY: 74344

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.0896

Alfa AF: 0.0888 Hom.: 104

Bravo AF: 0.103

Asia WGS AF: 0.212 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs13010022; hg19: chr2-38909706;