dbSNP rs929039: LGALS1:c.-199T>A (chr22-37675504-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002305.4(LGALS1):c.-199T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000256 in 390,356 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000026 ( 0 hom. )

Consequence

LGALS1
NM_002305.4 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

Publications

0 publications found

Variant links:

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]

LGALS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGALS1	NM_002305.4 link	c.-199T>A		upstream_gene_variant		ENST00000215909.10	NP_002296.1	P09382A0A384MR27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS1	ENST00000215909.10 link	c.-199T>A		upstream_gene_variant		1	NM_002305.4	ENSP00000215909.5		P09382

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000256

AC:

AN:

390356

Hom.:

AF XY:

0.00

AC XY:

AN XY:

206394

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

9448

American (AMR)

AF:

0.00

AC:

AN:

14080

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12014

East Asian (EAS)

AF:

0.00

AC:

AN:

25198

South Asian (SAS)

AF:

0.00

AC:

AN:

38278

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28096

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1700

European-Non Finnish (NFE)

AF:

0.00000418

AC:

AN:

239018

Other (OTH)

AF:

0.00

AC:

AN:

22524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

2.0

(source)

DANN

Benign

0.80

PhyloP100

-1.3

PromoterAI

0.11

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over