rs73933062

Positions:

• chr19-38812794-C-T

Variant summary

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

The NM_006149.4(LGALS4):​c.45+48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,597,778 control chromosomes in the GnomAD database, including 13,401 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 0.092 (849 hom., cov: 32)
  • Exomes 𝑓: 0.13 (12552 hom.)
• Consequence: LGALS4 NM_006149.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483

Genes affected

LGALS4 (HGNC:6565): (galectin 4) The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. The expression of this gene is restricted to small intestine, colon, and rectum, and it is underexpressed in colorectal cancer. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGALS4	NM_006149.4	c.45+48G>A		intron_variant		ENST00000307751.9
LGALS4	XM_011526973.3	c.45+48G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LGALS4	ENST00000307751.9	c.45+48G>A		intron_variant		1	NM_006149.4	P1

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13961 AN: 152082 Hom.: 851 Cov.: 32

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.101

GnomAD3 exomes AF: 0.118 AC: 28855 AN: 244550 Hom.: 2080 AF XY: 0.126 AC XY: 16767 AN XY: 132580

Gnomad AFR exome AF: 0.0215

Gnomad AMR exome AF: 0.101

Gnomad ASJ exome AF: 0.126

Gnomad EAS exome AF: 0.00272

Gnomad SAS exome AF: 0.203

Gnomad FIN exome AF: 0.0908

Gnomad NFE exome AF: 0.136

Gnomad OTH exome AF: 0.131

GnomAD4 exome AF: 0.126 AC: 182104 AN: 1445578 Hom.: 12552 Cov.: 29 AF XY: 0.129 AC XY: 92991 AN XY: 719986

Gnomad4 AFR exome AF: 0.0215

Gnomad4 AMR exome AF: 0.0988

Gnomad4 ASJ exome AF: 0.124

Gnomad4 EAS exome AF: 0.00159

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.0929

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.0918 AC: 13965 AN: 152200 Hom.: 849 Cov.: 32 AF XY: 0.0921 AC XY: 6854 AN XY: 74404

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.102

Alfa AF: 0.115 Hom.: 218

Bravo AF: 0.0866

Asia WGS AF: 0.0970 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.48

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: rs73933062; hg19: chr19-39303434; COSMIC: COSV55489071; COSMIC: COSV55489071;