rs1723527

Variant names:

• chr6-63391913-A-G
• rs1723527
• XM_017010930.3:c.-650-9357T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-63391913-A-G
• chr6-63391913-A-T

Variant summary

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

The XM_017010930.3(LGSN):​c.-650-9357T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,170 control chromosomes in the GnomAD database, including 4,813 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 0.18 (4813 hom., cov: 32)
• Consequence: LGSN XM_017010930.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGSN	XM_017010930.3	c.-650-9357T>C		intron_variant	Intron 2 of 9		XP_016866419.1
LGSN	XM_047418866.1	c.-651+624T>C		intron_variant	Intron 4 of 11		XP_047274822.1
LGSN	XM_011535892.4	c.-665-9357T>C		intron_variant	Intron 2 of 9		XP_011534194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289911	ENST00000701584.1	n.309-9357T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27953 AN: 152052 Hom.: 4782 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0672

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.184 AC: 28045 AN: 152170 Hom.: 4813 Cov.: 32 AF XY: 0.180 AC XY: 13431 AN XY: 74422

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0672

Gnomad4 EAS AF: 0.0615

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0480

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0925 Hom.: 1089

Bravo AF: 0.201

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.36
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1723527; hg19: chr6-64101818;