rs9449312

Variant names:

• chr6-63459629-A-C
• rs9449312
• XM_047418866.1:c.-963-15871T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-63459629-A-C
• chr6-63459629-A-G

Variant summary

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

The XM_047418866.1(LGSN):​c.-963-15871T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,610 control chromosomes in the GnomAD database, including 22,255 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 0.54 (22255 hom., cov: 29)
• Consequence: LGSN XM_047418866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

LGSN (HGNC:21016): (lengsin, lens protein with glutamine synthetase domain) This gene encodes a protein with similarity to the GS I members of the glutamine synthetase superfamily. The encoded protein is referred to as a pseudo-glutamine synthetase because it has no glutamine synthesis activity and may function as a chaperone protein. This protein is localized to the lens and may be associated with cataract disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]

ENSG00000289911 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGSN	XM_047418866.1	c.-963-15871T>G		intron_variant	Intron 1 of 11		XP_047274822.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289911	ENST00000701584.1	n.134-15871T>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81544 AN: 151492 Hom.: 22249 Cov.: 29

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.538 AC: 81585 AN: 151610 Hom.: 22255 Cov.: 29 AF XY: 0.539 AC XY: 39887 AN XY: 74032

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.560

Alfa AF: 0.569 Hom.: 40589

Bravo AF: 0.526

Asia WGS AF: 0.583 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.086
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9449312; hg19: chr6-64169534;