rs9622682

chr22-37678427-G-Achr22-37678427-G-T

Variant summary

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

The NM_002305.4(LGALS1):c.90-56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,582,550 control chromosomes in the GnomAD database, including 156,039 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 0.48 (18374 hom., cov: 32)
  • Exomes 𝑓: 0.44 (137665 hom.)
• Consequence: LGALS1 NM_002305.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

LGALS1 (HGNC:6561): (galectin 1) The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. This gene product may act as an autocrine negative growth factor that regulates cell proliferation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGALS1	NM_002305.4	c.90-56G>A		intron_variant		ENST00000215909.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LGALS1	ENST00000215909.10	c.90-56G>A		intron_variant		1	NM_002305.4	P1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73492 AN: 151962 Hom.: 18363 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.481

GnomAD3 exomes AF: 0.447 AC: 106582 AN: 238308 Hom.: 24097 AF XY: 0.444 AC XY: 57552 AN XY: 129650

Gnomad AFR exome AF: 0.628

Gnomad AMR exome AF: 0.433

Gnomad ASJ exome AF: 0.515

Gnomad EAS exome AF: 0.512

Gnomad SAS exome AF: 0.431

Gnomad FIN exome AF: 0.384

Gnomad NFE exome AF: 0.426

Gnomad OTH exome AF: 0.444

GnomAD4 exome AF: 0.437 AC: 625004 AN: 1430470 Hom.: 137665 Cov.: 26 AF XY: 0.436 AC XY: 310469 AN XY: 712710

Gnomad4 AFR exome AF: 0.633

Gnomad4 AMR exome AF: 0.436

Gnomad4 ASJ exome AF: 0.512

Gnomad4 EAS exome AF: 0.518

Gnomad4 SAS exome AF: 0.427

Gnomad4 FIN exome AF: 0.386

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.452

GnomAD4 genome AF: 0.484 AC: 73542 AN: 152080 Hom.: 18374 Cov.: 32 AF XY: 0.480 AC XY: 35678 AN XY: 74352

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.479

Alfa AF: 0.455 Hom.: 4744

Bravo AF: 0.495

Asia WGS AF: 0.477 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.47
Dann	Benign	0.66

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: rs9622682; hg19: chr22-38074434;