chr3-319864-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006614.4(CHL1):c.88T>G(p.Ser30Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00205 in 1,559,796 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 19 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 25 hom. )
Consequence
CHL1
NM_006614.4 missense
NM_006614.4 missense
Scores
1
15
Clinical Significance
Conservation
PhyloP100: 4.38
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0055780113).
BP6
?
Variant 3-319864-T-G is Benign according to our data. Variant chr3-319864-T-G is described in ClinVar as [Benign]. Clinvar id is 767882.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00894 (1360/152136) while in subpopulation AFR AF= 0.03 (1245/41546). AF 95% confidence interval is 0.0286. There are 19 homozygotes in gnomad4. There are 656 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 19 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHL1 | NM_006614.4 | c.88T>G | p.Ser30Ala | missense_variant | 3/28 | ENST00000256509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHL1 | ENST00000256509.7 | c.88T>G | p.Ser30Ala | missense_variant | 3/28 | 1 | NM_006614.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00885 AC: 1345AN: 152018Hom.: 19 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1345
AN:
152018
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00289 AC: 706AN: 243914Hom.: 9 AF XY: 0.00279 AC XY: 368AN XY: 131956
GnomAD3 exomes
AF:
AC:
706
AN:
243914
Hom.:
AF XY:
AC XY:
368
AN XY:
131956
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00130 AC: 1834AN: 1407660Hom.: 25 Cov.: 23 AF XY: 0.00140 AC XY: 983AN XY: 703088
GnomAD4 exome
AF:
AC:
1834
AN:
1407660
Hom.:
Cov.:
23
AF XY:
AC XY:
983
AN XY:
703088
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00894 AC: 1360AN: 152136Hom.: 19 Cov.: 32 AF XY: 0.00882 AC XY: 656AN XY: 74362
GnomAD4 genome
?
AF:
AC:
1360
AN:
152136
Hom.:
Cov.:
32
AF XY:
AC XY:
656
AN XY:
74362
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
103
ESP6500EA
AF:
AC:
0
ExAC
?
AF:
AC:
437
Asia WGS
AF:
AC:
28
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;.
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;.
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
B;B;.;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at