14-55138098-C-T

Variant names:

• chr14-55138098-C-T
• rs181337247
• NM_002306.4:c.72C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_002306.4(LGALS3):​c.72C>T​(p.Gly24Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000625 in 1,530,868 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00041 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00065 (1 hom.)
• Consequence: LGALS3 NM_002306.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.68
• Publications: 0 publications found

Genes affected

LGALS3 (HGNC:6563): (galectin 3) This gene encodes a member of the galectin family of carbohydrate binding proteins. Members of this protein family have an affinity for beta-galactosides. The encoded protein is characterized by an N-terminal proline-rich tandem repeat domain and a single C-terminal carbohydrate recognition domain. This protein can self-associate through the N-terminal domain allowing it to bind to multivalent saccharide ligands. This protein localizes to the extracellular matrix, the cytoplasm and the nucleus. This protein plays a role in numerous cellular functions including apoptosis, innate immunity, cell adhesion and T-cell regulation. The protein exhibits antimicrobial activity against bacteria and fungi. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2014]

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 14-55138098-C-T is Benign according to our data. Variant chr14-55138098-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2644252.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.68 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002306.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS3	NM_002306.4	MANE Select	c.72C>T	p.Gly24Gly	synonymous	Exon 3 of 6	NP_002297.2	P17931
	LGALS3	NM_001357678.2		c.114C>T	p.Gly38Gly	synonymous	Exon 4 of 7	NP_001344607.1
	LGALS3	NR_003225.2		n.1116C>T		non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS3	ENST00000254301.14	TSL:1 MANE Select	c.72C>T	p.Gly24Gly	synonymous	Exon 3 of 6	ENSP00000254301.9	P17931
	LGALS3	ENST00000556438.6	TSL:1	n.911C>T		non_coding_transcript_exon	Exon 1 of 4
	LGALS3	ENST00000947958.1		c.213C>T	p.Gly71Gly	synonymous	Exon 4 of 7	ENSP00000618017.1

Frequencies

GnomAD3 genomes AF: 0.000414 AC: 63 AN: 152192 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000750

Gnomad OTH AF: 0.00144

GnomAD2 exomes AF: 0.000332 AC: 62 AN: 186510 AF XY: 0.000269

Gnomad AFR exome AF: 0.0000686

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000324

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000612

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000649 AC: 894 AN: 1378558 Hom.: 1 Cov.: 31 AF XY: 0.000639 AC XY: 433 AN XY: 678030

African (AFR) AF: 0.0000987 AC: 3 AN: 30402

American (AMR) AF: 0.00 AC: 0 AN: 29446

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20812

East Asian (EAS) AF: 0.000180 AC: 7 AN: 38874

South Asian (SAS) AF: 0.00 AC: 0 AN: 71640

European-Finnish (FIN) AF: 0.0000198 AC: 1 AN: 50462

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5386

European-Non Finnish (NFE) AF: 0.000756 AC: 813 AN: 1074866

Other (OTH) AF: 0.00124 AC: 70 AN: 56670

GnomAD4 genome AF: 0.000414 AC: 63 AN: 152310 Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29 AN XY: 74476

African (AFR) AF: 0.000120 AC: 5 AN: 41566

American (AMR) AF: 0.00 AC: 0 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000750 AC: 51 AN: 68018

Other (OTH) AF: 0.00142 AC: 3 AN: 2112

Alfa AF: 0.000451 Hom.: 0

Bravo AF: 0.000336

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs181337247; hg19: chr14-55604816;