rs11706690

chr3-381335-C-Achr3-381335-C-G

Variant summary

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

The NM_006614.4(CHL1):c.1877-844C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,990 control chromosomes in the GnomAD database, including 23,689 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 0.51 (23689 hom., cov: 31)
• Consequence: CHL1 NM_006614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

CHL1 (HGNC:1939): (cell adhesion molecule L1 like) The protein encoded by this gene is a member of the L1 gene family of neural cell adhesion molecules. It is a neural recognition molecule that may be involved in signal transduction pathways. The deletion of one copy of this gene may be responsible for mental defects in patients with 3p- syndrome. This protein may also play a role in the growth of certain cancers. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Nov 2011]

CHL1-AS1 (HGNC:40148): (CHL1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHL1	NM_006614.4	c.1877-844C>A		intron_variant		ENST00000256509.7
CHL1-AS1	NR_110739.1	n.259+1232G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHL1	ENST00000256509.7	c.1877-844C>A		intron_variant		1	NM_006614.4	P3
CHL1-AS1	ENST00000417612.1	n.259+1232G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78202 AN: 151870 Hom.: 23685 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.515 AC: 78221 AN: 151990 Hom.: 23689 Cov.: 31 AF XY: 0.521 AC XY: 38729 AN XY: 74274

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.537

Alfa AF: 0.629 Hom.: 39148

Bravo AF: 0.484

Asia WGS AF: 0.636 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.9
Dann	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11706690; hg19: chr3-423018;