rs567481251

Variant names:

• chr17-20450102-T-C
• rs567481251
• NM_001367292.2:c.942A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-20450102-T-C
• chr17-20450102-T-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001367292.2(LGALS9B):​c.942A>G​(p.Glu314Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.000047 (0 hom., cov: 15)
  • Exomes 𝑓: 0.0000012 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LGALS9B NM_001367292.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

LGALS9B (HGNC:24842): (galectin 9B) This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more centromeric gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=-0.128 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGALS9B	NM_001367292.2	c.942A>G	p.Glu314Glu	synonymous_variant	Exon 11 of 11	ENST00000423676.8	NP_001354221.1
LGALS9B	NM_001042685.3	c.939A>G	p.Glu313Glu	synonymous_variant	Exon 11 of 11		NP_001036150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS9B	ENST00000423676.8	c.942A>G	p.Glu314Glu	synonymous_variant	Exon 11 of 11	1	NM_001367292.2	ENSP00000388841.3
LGALS9B	ENST00000324290.5	c.939A>G	p.Glu313Glu	synonymous_variant	Exon 11 of 11	5		ENSP00000315564.5
LGALS9B	ENST00000578481.5	n.*742A>G		non_coding_transcript_exon_variant	Exon 10 of 10	2		ENSP00000464627.1
LGALS9B	ENST00000578481.5	n.*742A>G		3_prime_UTR_variant	Exon 10 of 10	2		ENSP00000464627.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 5 AN: 106066 Hom.: 0 Cov.: 15 FAILED QC

Gnomad AFR AF: 0.000130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000221

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000116 AC: 1 AN: 858516 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 436460

Gnomad4 AFR exome AF: 0.0000394

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000471 AC: 5 AN: 106066 Hom.: 0 Cov.: 15 AF XY: 0.0000584 AC XY: 3 AN XY: 51404

Gnomad4 AFR AF: 0.000130

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000221

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs567481251; hg19: chr17-20353415;