rs330891

Positions:

• chr3-329477-G-A
• chr3-329477-G-C
• chr3-329477-G-T

Variant summary

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

The NM_006614.4(CHL1):​c.385+1123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,864 control chromosomes in the GnomAD database, including 42,323 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 0.74 (42323 hom., cov: 31)
• Consequence: CHL1 NM_006614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHL1	NM_006614.4	c.385+1123G>A		intron_variant		ENST00000256509.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHL1	ENST00000256509.7	c.385+1123G>A		intron_variant		1	NM_006614.4	P3

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112821 AN: 151746 Hom.: 42300 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.743 AC: 112897 AN: 151864 Hom.: 42323 Cov.: 31 AF XY: 0.741 AC XY: 54982 AN XY: 74170

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.751

Alfa AF: 0.777 Hom.: 19955

Bravo AF: 0.738

Asia WGS AF: 0.676 AC: 2343 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.30

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: rs330891; hg19: chr3-371160;