rs782713149

chrX-153869665-T-TGTGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001278116.2(L1CAM):c.1124-3_1124-2insGCAC variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,093,138 control chromosomes in the GnomAD database, including 1 homozygotes. There are 23 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.000040 (1 hom. 23 hem.)
• Consequence: L1CAM NM_001278116.2 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1 B:1
• Conservation: PhyloP100: 1.13

Genes affected

L1CAM (HGNC:6470): (L1 cell adhesion molecule) The protein encoded by this gene is an axonal glycoprotein belonging to the immunoglobulin supergene family. The ectodomain, consisting of several immunoglobulin-like domains and fibronectin-like repeats (type III), is linked via a single transmembrane sequence to a conserved cytoplasmic domain. This cell adhesion molecule plays an important role in nervous system development, including neuronal migration and differentiation. Mutations in the gene cause X-linked neurological syndromes known as CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia and hydrocephalus). Alternative splicing of this gene results in multiple transcript variants, some of which include an alternate exon that is considered to be specific to neurons. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Hemizygotes in GnomAdExome at 5 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
L1CAM	NM_001278116.2	c.1124-3_1124-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000370060.7
L1CAM	NM_000425.5	c.1124-3_1124-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
L1CAM	NM_001143963.2	c.1109-3_1109-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
L1CAM	NM_024003.3	c.1124-3_1124-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
L1CAM	ENST00000370060.7	c.1124-3_1124-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_001278116.2	A1
L1CAM	ENST00000361699.8	c.1124-3_1124-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		P4
L1CAM	ENST00000361981.7	c.1109-3_1109-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		A1
L1CAM	ENST00000370055.5	c.1109-3_1109-2insGCAC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5		A1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD3 exomes AF: 0.0000712 AC: 12 AN: 168449 Hom.: 1 AF XY: 0.0000888 AC XY: 5 AN XY: 56285

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000693

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000403 AC: 44 AN: 1093138 Hom.: 1 Cov.: 33 AF XY: 0.0000640 AC XY: 23 AN XY: 359410

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000790

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000436

GnomAD4 genome Cov.: 24

Bravo AF: 0.00000378

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

research

Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre

-

- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 04, 2023

- -

Spastic paraplegia Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 10, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs782713149; hg19: chrX-153135120;