rs12167604

Positions:

• chr22-37678135-T-C
• chr22-37678135-T-G

Variant summary

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

The ENST00000215909.10(LGALS1):​c.90-348T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,002 control chromosomes in the GnomAD database, including 18,443 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 (18443 hom., cov: 32)
• Consequence: LGALS1 ENST00000215909.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALS1	NM_002305.4	c.90-348T>C		intron_variant		ENST00000215909.10	NP_002296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS1	ENST00000215909.10	c.90-348T>C		intron_variant		1	NM_002305.4	ENSP00000215909	P1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73573 AN: 151884 Hom.: 18432 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.515

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: 0.426

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.484 AC: 73623 AN: 152002 Hom.: 18443 Cov.: 32 AF XY: 0.481 AC XY: 35719 AN XY: 74310

Gnomad4 AFR AF: 0.625

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: 0.426

Gnomad4 OTH AF: 0.479

Alfa AF: 0.469 Hom.: 4321

Bravo AF: 0.496

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.39

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: rs12167604; hg19: chr22-38074142;