rs929039

Variant names:

• chr22-37675504-T-A
• rs929039
• NM_002305.4:c.-199T>A

Your query was ambiguous. Multiple possible variants found:

• chr22-37675504-T-A
• chr22-37675504-T-C
• chr22-37675504-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 0 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: 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).

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.-199T>A		upstream_gene	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.-199T>A		upstream_gene	N/A	ENSP00000215909.5
	LGALS1	ENST00000425542.5	TSL:3	n.-199T>A		upstream_gene	N/A	ENSP00000404414.1
	LGALS1	ENST00000454173.1	TSL:5	n.-199T>A		upstream_gene	N/A	ENSP00000388296.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000256 AC: 1 AN: 390356 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 206394

African (AFR) AF: 0.00 AC: 0 AN: 9448

American (AMR) AF: 0.00 AC: 0 AN: 14080

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12014

East Asian (EAS) AF: 0.00 AC: 0 AN: 25198

South Asian (SAS) AF: 0.00 AC: 0 AN: 38278

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28096

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1700

European-Non Finnish (NFE) AF: 0.00000418 AC: 1 AN: 239018

Other (OTH) AF: 0.00 AC: 0 AN: 22524

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	2.0
DANN	Benign	0.80
PhyloP100		-1.3
PromoterAI		0.11	Neutral

Splicing

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

Other links and lift over

dbSNP: rs929039; hg19: chr22-38071511;