rs2677024

Positions:

• chr6-63374900-G-A

Variant summary

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

The XM_017010930.3(LGSN):​c.-288+4396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,970 control chromosomes in the GnomAD database, including 2,454 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 0.12 (2454 hom., cov: 32)
• Consequence: LGSN XM_017010930.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LGSN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGSN	XM_011535892.4	c.-303+4396C>T		intron_variant			XP_011534194.1
LGSN	XM_017010930.3	c.-288+4396C>T		intron_variant			XP_016866419.1
LGSN	XM_047418866.1	c.-288+4396C>T		intron_variant			XP_047274822.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18380 AN: 151852 Hom.: 2440 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.121 AC: 18438 AN: 151970 Hom.: 2454 Cov.: 32 AF XY: 0.118 AC XY: 8777 AN XY: 74292

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.0690

Gnomad4 ASJ AF: 0.0279

Gnomad4 EAS AF: 0.0972

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0449 Hom.: 570

Bravo AF: 0.134

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2677024; hg19: chr6-64084805;