rs7291467

chr22-37576621-G-A

Variant summary

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

The NM_006498.3(LGALS2):c.6+3279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,890 control chromosomes in the GnomAD database, including 19,847 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.49 (19847 hom., cov: 31)
• Consequence: LGALS2 NM_006498.3 intron
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.68

Genes affected

LGALS2 (HGNC:6562): (galectin 2) The protein encoded by this gene is a soluble beta-galactoside binding lectin. The encoded protein is found as a homodimer and can bind to lymphotoxin-alpha. A single nucleotide polymorphism in an intron of this gene can alter the transcriptional level of the protein, with a resultant increased risk of myocardial infarction. [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 (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGALS2	NM_006498.3	c.6+3279C>T		intron_variant		ENST00000215886.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LGALS2	ENST00000215886.6	c.6+3279C>T		intron_variant		1	NM_006498.3	P1
LGALS2	ENST00000416480.1	c.6+3279C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74892 AN: 151772 Hom.: 19842 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.493 AC: 74922 AN: 151890 Hom.: 19847 Cov.: 31 AF XY: 0.499 AC XY: 37058 AN XY: 74246

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.481

Alfa AF: 0.547 Hom.: 4730

Bravo AF: 0.475

Asia WGS AF: 0.445 AC: 1544 AN: 3476

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Myocardial infarction, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

May 06, 2004

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.66
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: rs7291467; hg19: chr22-37972628;