rs7291467

Variant names:

• chr22-37576621-G-A
• rs7291467
• NM_006498.3:c.6+3279C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 40 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006498.3. 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
	LGALS2	NM_006498.3	MANE Select	c.6+3279C>T		intron	N/A	NP_006489.1	P05162

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS2	ENST00000215886.6	TSL:1 MANE Select	c.6+3279C>T		intron	N/A	ENSP00000215886.4	P05162
	LGALS2	ENST00000416480.1	TSL:3	c.6+3279C>T		intron	N/A	ENSP00000407351.1	B0QYC9

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

African (AFR) AF: 0.307 AC: 12702 AN: 41412

American (AMR) AF: 0.547 AC: 8349 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1540 AN: 5152

South Asian (SAS) AF: 0.558 AC: 2684 AN: 4806

European-Finnish (FIN) AF: 0.666 AC: 7045 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39689 AN: 67910

Other (OTH) AF: 0.481 AC: 1013 AN: 2106

Alfa AF: 0.547 Hom.: 4730

Bravo AF: 0.475

Asia WGS AF: 0.445 AC: 1544 AN: 3476

ClinVar

ClinVar submissions

Significance: risk factor

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Myocardial infarction, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.61
PhyloP100		-1.7
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: rs7291467; hg19: chr22-37972628;