rs2239679

Positions:

• chr11-63511149-C-G
• chr11-63511149-C-T

Variant summary

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

The NM_033101.4(LGALS12):​c.558+44C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 1,587,202 control chromosomes in the GnomAD database, including 201,224 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 0.40 (14777 hom., cov: 33)
  • Exomes 𝑓: 0.50 (186447 hom.)
• Consequence: LGALS12 NM_033101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

LGALS12 (HGNC:15788): (galectin 12) This gene encodes a member of the galectin superfamily, a group of beta-galactoside-binding proteins with conserved carbohydrate recognition domains. The related mouse protein is a primary regulator of the early stages of adipose tissue development. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALS12	NM_033101.4	c.558+44C>G		intron_variant		ENST00000394618.9	NP_149092.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS12	ENST00000394618.9	c.558+44C>G		intron_variant		1	NM_033101.4	ENSP00000378116	P4

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61028 AN: 151970 Hom.: 14775 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.380

GnomAD3 exomes AF: 0.463 AC: 114899 AN: 248012 Hom.: 28617 AF XY: 0.468 AC XY: 62797 AN XY: 134318

Gnomad AFR exome AF: 0.135

Gnomad AMR exome AF: 0.508

Gnomad ASJ exome AF: 0.418

Gnomad EAS exome AF: 0.207

Gnomad SAS exome AF: 0.422

Gnomad FIN exome AF: 0.613

Gnomad NFE exome AF: 0.528

Gnomad OTH exome AF: 0.471

GnomAD4 exome AF: 0.501 AC: 719609 AN: 1435114 Hom.: 186447 Cov.: 28 AF XY: 0.500 AC XY: 358034 AN XY: 715538

Gnomad4 AFR exome AF: 0.121

Gnomad4 AMR exome AF: 0.496

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.253

Gnomad4 SAS exome AF: 0.424

Gnomad4 FIN exome AF: 0.610

Gnomad4 NFE exome AF: 0.528

Gnomad4 OTH exome AF: 0.461

GnomAD4 genome AF: 0.401 AC: 61052 AN: 152088 Hom.: 14777 Cov.: 33 AF XY: 0.407 AC XY: 30283 AN XY: 74338

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.380

Alfa AF: 0.466 Hom.: 3238

Bravo AF: 0.378

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.52

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: rs2239679; hg19: chr11-63278621; COSMIC: COSV55370490;