rs149949698

Variant names:

• chr2-38675812-G-A
• rs149949698
• NM_138801.3:c.191-100G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-38675812-G-A
• chr2-38675812-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138801.3(GALM):​c.191-100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000486 in 1,069,374 control chromosomes in the GnomAD database, including 1 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 0.000040 (0 hom., cov: 30)
  • Exomes 𝑓: 0.000050 (1 hom.)
• Consequence: GALM NM_138801.3 intron
• Clinical Significance: Not reported in ClinVar
• 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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALM	NM_138801.3	c.191-100G>A		intron_variant	Intron 1 of 6	ENST00000272252.10	NP_620156.1
GALM	XM_011532540.3	c.191-100G>A		intron_variant	Intron 1 of 5		XP_011530842.1
GALM	XM_047443419.1	c.191-100G>A		intron_variant	Intron 1 of 5		XP_047299375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALM	ENST00000272252.10	c.191-100G>A		intron_variant	Intron 1 of 6	1	NM_138801.3	ENSP00000272252.5
GALM	ENST00000410063.5	c.190+9461G>A		intron_variant	Intron 1 of 3	3		ENSP00000386233.1
GALM	ENST00000427858.4	n.272-100G>A		intron_variant	Intron 1 of 3	4
GALM	ENST00000444351.5	n.110-100G>A		intron_variant	Intron 1 of 6	5		ENSP00000409083.1

Frequencies

GnomAD3 genomes AF: 0.0000395 AC: 6 AN: 151772 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000263

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000501 AC: 46 AN: 917602 Hom.: 1 AF XY: 0.0000444 AC XY: 21 AN XY: 472528

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000957

Gnomad4 ASJ exome AF: 0.0000502

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000144

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000787

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000395 AC: 6 AN: 151772 Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2 AN XY: 74136

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000263

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.61

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: rs149949698; hg19: chr2-38902954;