6-63480541-C-T

Position:

• chr6-63480541-C-T

Variant summary

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

The XM_047418866.1(LGSN):​c.-963-36783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,346 control chromosomes in the GnomAD database, including 18,329 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 (18148 hom., cov: 30)
  • Exomes 𝑓: 0.66 (181 hom.)
• Consequence: LGSN XM_047418866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81

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]

EEF1B2P5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• 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/exons	MANE	Protein	UniProt
LGSN	XM_047418866.1	c.-963-36783G>A		intron_variant			XP_047274822.1
EEF1B2P5		n.63480541C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1B2P5	ENST00000444820.2	n.408C>T		non_coding_transcript_exon_variant	1/2	6
ENSG00000289911	ENST00000701584.1	n.134-36783G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70363 AN: 151444 Hom.: 18157 Cov.: 30

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.659 AC: 522 AN: 792 Hom.: 181 Cov.: 0 AF XY: 0.673 AC XY: 268 AN XY: 398

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.669

Gnomad4 NFE exome AF: 0.621

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.464 AC: 70354 AN: 151554 Hom.: 18148 Cov.: 30 AF XY: 0.468 AC XY: 34656 AN XY: 74044

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.507

Alfa AF: 0.534 Hom.: 9846

Bravo AF: 0.442

Asia WGS AF: 0.547 AC: 1903 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	1.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4299811; hg19: chr6-64190446;