rs9353016

Variant names:

• chr6-63476127-G-A
• rs9353016
• ENST00000701584.1:n.134-32369C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-63476127-G-A
• chr6-63476127-G-C

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.134-32369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,946 control chromosomes in the GnomAD database, including 18,196 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 0.46 (18196 hom., cov: 32)
• Consequence: ENSG00000289911 ENST00000701584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGSN	XM_047418866.1	c.-963-32369C>T		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.134-32369C>T		intron_variant	Intron 1 of 5
ENSG00000289911	ENST00000825503.1	n.131-32369C>T		intron_variant	Intron 1 of 3
ENSG00000289911	ENST00000825504.1	n.146-32369C>T		intron_variant	Intron 1 of 5
ENSG00000289911	ENST00000825505.1	n.93-32369C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70534 AN: 151828 Hom.: 18205 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.464 AC: 70529 AN: 151946 Hom.: 18196 Cov.: 32 AF XY: 0.468 AC XY: 34757 AN XY: 74250

African (AFR) AF: 0.228 AC: 9469 AN: 41444

American (AMR) AF: 0.464 AC: 7067 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2205 AN: 3464

East Asian (EAS) AF: 0.549 AC: 2837 AN: 5166

South Asian (SAS) AF: 0.513 AC: 2473 AN: 4822

European-Finnish (FIN) AF: 0.618 AC: 6517 AN: 10552

Middle Eastern (MID) AF: 0.541 AC: 157 AN: 290

European-Non Finnish (NFE) AF: 0.564 AC: 38324 AN: 67952

Other (OTH) AF: 0.505 AC: 1065 AN: 2110

Alfa AF: 0.529 Hom.: 70575

Bravo AF: 0.443

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9353016; hg19: chr6-64186032;