rs1373131590

Variant names:

• chr3-328209-C-G
• NM_006614.4:c.240C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-328209-C-G
• chr3-328209-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006614.4(CHL1):​c.240C>G​(p.Asp80Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,456,492 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: CHL1 NM_006614.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHL1	NM_006614.4	c.240C>G	p.Asp80Glu	missense_variant	Exon 5 of 28	ENST00000256509.7	NP_006605.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHL1	ENST00000256509.7	c.240C>G	p.Asp80Glu	missense_variant	Exon 5 of 28	1	NM_006614.4	ENSP00000256509.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1456492 Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2 AN XY: 724560

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: 0.0000117

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.030
CADD	Benign	11
DANN	Uncertain	0.99
DEOGEN2	Benign	0.17	.;T;.;.;T;.
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.56
FATHMM_MKL	Benign	0.33	N
LIST_S2	Benign	0.70	T;T;T;T;T;T
M_CAP	Uncertain	0.21	D
MetaRNN	Uncertain	0.56	D;D;D;D;D;D
MetaSVM	Uncertain	0.67	D
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-2.2	N;N;D;D;N;.
REVEL	Uncertain	0.52
Sift	Uncertain	0.0040	D;D;D;T;D;.
Sift4G	Uncertain	0.026	D;T;D;T;D;T
Polyphen		0.98	D;D;.;.;.;.
Vest4		0.55
MutPred		0.53		Gain of glycosylation at T79 (P = 0.058);Gain of glycosylation at T79 (P = 0.058);Gain of glycosylation at T79 (P = 0.058);Gain of glycosylation at T79 (P = 0.058);Gain of glycosylation at T79 (P = 0.058);Gain of glycosylation at T79 (P = 0.058);
MVP		0.67
MPC		0.072
ClinPred		0.98	D
GERP RS		-4.6
Varity_R		0.23
gMVP		0.54

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-369892;