rs2239679

Variant names:

• chr11-63511149-C-G
• rs2239679
• NM_033101.4:c.558+44C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000394618.9(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 ENST00000394618.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000394618.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS12	NM_033101.4	MANE Select	c.558+44C>G		intron	N/A	NP_149092.3
	LGALS12	NM_001142535.2		c.561+44C>G		intron	N/A	NP_001136007.2
	LGALS12	NM_001142536.2		c.532-603C>G		intron	N/A	NP_001136008.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS12	ENST00000394618.9	TSL:1 MANE Select	c.558+44C>G		intron	N/A	ENSP00000378116.4
	LGALS12	ENST00000340246.10	TSL:1	c.561+44C>G		intron	N/A	ENSP00000339374.6
	LGALS12	ENST00000255684.10	TSL:1	c.532-603C>G		intron	N/A	ENSP00000255684.6

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

GnomAD2 exomes AF: 0.463 AC: 114899 AN: 248012 AF XY: 0.468

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 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

African (AFR) AF: 0.121 AC: 4010 AN: 33030

American (AMR) AF: 0.496 AC: 22162 AN: 44660

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 10881 AN: 26010

East Asian (EAS) AF: 0.253 AC: 10004 AN: 39600

South Asian (SAS) AF: 0.424 AC: 36427 AN: 85838

European-Finnish (FIN) AF: 0.610 AC: 30026 AN: 49214

Middle Eastern (MID) AF: 0.379 AC: 2175 AN: 5738

European-Non Finnish (NFE) AF: 0.528 AC: 576454 AN: 1091404

Other (OTH) AF: 0.461 AC: 27470 AN: 59620

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

African (AFR) AF: 0.139 AC: 5775 AN: 41528

American (AMR) AF: 0.461 AC: 7042 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1069 AN: 5166

South Asian (SAS) AF: 0.411 AC: 1983 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6565 AN: 10546

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35810 AN: 67966

Other (OTH) AF: 0.380 AC: 802 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.52
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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