rs9622682

Variant names:

• chr22-37678427-G-A
• rs9622682
• NM_002305.4:c.90-56G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-37678427-G-A
• chr22-37678427-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002305.4. 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
	LGALS1	NM_002305.4	MANE Select	c.90-56G>A		intron	N/A	NP_002296.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS1	ENST00000215909.10	TSL:1 MANE Select	c.90-56G>A		intron	N/A	ENSP00000215909.5
	LGALS1	ENST00000472321.1	TSL:2	n.119G>A		non_coding_transcript_exon	Exon 2 of 3
	LGALS1	ENST00000425542.5	TSL:3	n.*10-56G>A		intron	N/A	ENSP00000404414.1

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

GnomAD2 exomes AF: 0.447 AC: 106582 AN: 238308 AF XY: 0.444

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 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

African (AFR) AF: 0.633 AC: 20750 AN: 32762

American (AMR) AF: 0.436 AC: 19134 AN: 43878

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 13235 AN: 25864

East Asian (EAS) AF: 0.518 AC: 20283 AN: 39140

South Asian (SAS) AF: 0.427 AC: 36307 AN: 85000

European-Finnish (FIN) AF: 0.386 AC: 20098 AN: 52082

Middle Eastern (MID) AF: 0.439 AC: 2511 AN: 5724

European-Non Finnish (NFE) AF: 0.429 AC: 465878 AN: 1086678

Other (OTH) AF: 0.452 AC: 26808 AN: 59342

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

African (AFR) AF: 0.622 AC: 25816 AN: 41492

American (AMR) AF: 0.443 AC: 6778 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2537 AN: 5160

South Asian (SAS) AF: 0.426 AC: 2055 AN: 4826

European-Finnish (FIN) AF: 0.383 AC: 4046 AN: 10564

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28908 AN: 67966

Other (OTH) AF: 0.479 AC: 1012 AN: 2114

Alfa AF: 0.454 Hom.: 6981

Bravo AF: 0.495

Asia WGS AF: 0.477 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.47
DANN	Benign	0.66
PhyloP100		-1.9
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: rs9622682; hg19: chr22-38074434;