chr17-27646177-G-A

Variant names:

• chr17-27646177-G-A
• rs732222
• NM_009587.3:c.627+266G>A

Variant summary

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

The NM_009587.3(LGALS9):​c.627+266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,966 control chromosomes in the GnomAD database, including 4,739 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 0.25 (4739 hom., cov: 31)
• Consequence: LGALS9 NM_009587.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 10 publications found

Genes affected

LGALS9 (HGNC:6570): (galectin 9) The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. The protein encoded by this gene is an S-type lectin. It is overexpressed in Hodgkin's disease tissue and might participate in the interaction between the H&RS cells with their surrounding cells and might thus play a role in the pathogenesis of this disease and/or its associated immunodeficiency. Multiple alternatively spliced transcript variants have been found for this gene. [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 (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_009587.3. 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
	LGALS9	NM_009587.3	MANE Select	c.627+266G>A		intron	N/A	NP_033665.1
	LGALS9	NM_002308.4		c.531+266G>A		intron	N/A	NP_002299.2
	LGALS9	NM_001330163.2		c.531+266G>A		intron	N/A	NP_001317092.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS9	ENST00000395473.7	TSL:1 MANE Select	c.627+266G>A		intron	N/A	ENSP00000378856.2
	LGALS9	ENST00000302228.9	TSL:1	c.531+266G>A		intron	N/A	ENSP00000306228.5
	LGALS9	ENST00000481514.5	TSL:1	n.1336+266G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37652 AN: 151846 Hom.: 4734 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.248 AC: 37670 AN: 151966 Hom.: 4739 Cov.: 31 AF XY: 0.245 AC XY: 18224 AN XY: 74266

African (AFR) AF: 0.230 AC: 9530 AN: 41452

American (AMR) AF: 0.310 AC: 4737 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1314 AN: 5126

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2270 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16724 AN: 67936

Other (OTH) AF: 0.273 AC: 576 AN: 2110

Alfa AF: 0.246 Hom.: 594

Bravo AF: 0.256

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.61
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs732222; hg19: chr17-25973203;