rs9449312

Variant names:

• chr6-63459629-A-C
• rs9449312
• ENST00000701584.1:n.134-15871T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701584.1(ENSG00000289911):​n.134-15871T>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: ENSG00000289911 ENST00000701584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 3 publications found

Genes affected

ENSG00000289911 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000289911	ENST00000825503.1	n.131-15871T>G		intron_variant	Intron 1 of 3
ENSG00000289911	ENST00000825504.1	n.146-15871T>G		intron_variant	Intron 1 of 5
ENSG00000289911	ENST00000825505.1	n.93-15871T>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.475 AC: 19643 AN: 41322

American (AMR) AF: 0.493 AC: 7487 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2712 AN: 5114

South Asian (SAS) AF: 0.545 AC: 2614 AN: 4794

European-Finnish (FIN) AF: 0.618 AC: 6480 AN: 10490

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38655 AN: 67922

Other (OTH) AF: 0.560 AC: 1182 AN: 2110

Alfa AF: 0.559 Hom.: 64139

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9449312; hg19: chr6-64169534;