chr11-63517038-T-G

Variant names:

• chr11-63517038-T-G
• rs1404501
• ENST00000959022.1:c.*38-332T>G

Variant summary

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

The ENST00000959022.1(LGALS12):​c.*38-332T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,112 control chromosomes in the GnomAD database, including 3,753 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 0.18 (3753 hom., cov: 32)
• Consequence: LGALS12 ENST00000959022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000959022.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS12	ENST00000959022.1		c.*38-332T>G		intron	N/A	ENSP00000629081.1
	LGALS12	ENST00000959021.1		c.*37+608T>G		intron	N/A	ENSP00000629080.1
	LGALS12	ENST00000959023.1		c.*38-332T>G		intron	N/A	ENSP00000629082.1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28011 AN: 151994 Hom.: 3748 Cov.: 32

Gnomad AFR AF: 0.0447

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.184 AC: 28021 AN: 152112 Hom.: 3753 Cov.: 32 AF XY: 0.187 AC XY: 13933 AN XY: 74352

African (AFR) AF: 0.0445 AC: 1848 AN: 41510

American (AMR) AF: 0.261 AC: 3979 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3446 AN: 5170

South Asian (SAS) AF: 0.144 AC: 693 AN: 4802

European-Finnish (FIN) AF: 0.220 AC: 2328 AN: 10572

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14117 AN: 68006

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.115 Hom.: 262

Bravo AF: 0.189

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1404501; hg19: chr11-63284510;