rs1744134

Variant names:

• chr6-63494809-A-G
• rs1744134
• ENST00000701584.1:n.134-51051T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-63494809-A-G
• chr6-63494809-A-T

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.134-51051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,024 control chromosomes in the GnomAD database, including 7,910 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 0.32 (7910 hom., cov: 32)
• Consequence: ENSG00000289911 ENST00000701584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGSN	XM_047418866.1	c.-963-51051T>C		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.134-51051T>C		intron_variant	Intron 1 of 5
ENSG00000289911	ENST00000825503.1	n.131-51051T>C		intron_variant	Intron 1 of 3
ENSG00000289911	ENST00000825504.1	n.146-51051T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48527 AN: 151906 Hom.: 7903 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.319 AC: 48549 AN: 152024 Hom.: 7910 Cov.: 32 AF XY: 0.319 AC XY: 23676 AN XY: 74312

African (AFR) AF: 0.255 AC: 10586 AN: 41488

American (AMR) AF: 0.397 AC: 6062 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5178

South Asian (SAS) AF: 0.351 AC: 1691 AN: 4824

European-Finnish (FIN) AF: 0.279 AC: 2948 AN: 10558

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23471 AN: 67942

Other (OTH) AF: 0.333 AC: 703 AN: 2108

Alfa AF: 0.339 Hom.: 8041

Bravo AF: 0.325

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.39
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1744134; hg19: chr6-64204714;