rs10495881

Positions:

• chr2-38677850-A-G

Variant summary

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

The NM_138801.3(GALM):​c.345+1784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0618 in 151,804 control chromosomes in the GnomAD database, including 399 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 0.062 (399 hom., cov: 32)
• Consequence: GALM NM_138801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALM	NM_138801.3	c.345+1784A>G		intron_variant		ENST00000272252.10
GALM	XM_011532540.3	c.345+1784A>G		intron_variant
GALM	XM_047443419.1	c.345+1784A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALM	ENST00000272252.10	c.345+1784A>G		intron_variant		1	NM_138801.3	P1
GALM	ENST00000410063.5	c.190+11499A>G		intron_variant		3
GALM	ENST00000444351.5	c.264+1784A>G		intron_variant, NMD_transcript_variant		5
GALM	ENST00000427858.4	n.426+1784A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9368 AN: 151694 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0648

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

GnomAD4 genome AF: 0.0618 AC: 9381 AN: 151804 Hom.: 399 Cov.: 32 AF XY: 0.0624 AC XY: 4632 AN XY: 74192

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0416

Gnomad4 OTH AF: 0.0660

Alfa AF: 0.0519 Hom.: 159

Bravo AF: 0.0651

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.039
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs10495881; hg19: chr2-38904992;