rs62642468
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001764.3(CD1B):c.310G>A(p.Gly104Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,614,004 control chromosomes in the GnomAD database, including 160 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0099 ( 15 hom., cov: 32)
Exomes 𝑓: 0.013 ( 145 hom. )
Consequence
CD1B
NM_001764.3 missense
NM_001764.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.439
Genes affected
CD1B (HGNC:1635): (CD1b molecule) This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail, and requires vesicular acidification to bind lipid antigens. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0028293729).
BP6
?
Variant 1-158330814-C-T is Benign according to our data. Variant chr1-158330814-C-T is described in ClinVar as [Benign]. Clinvar id is 770494.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00987 (1503/152280) while in subpopulation AMR AF= 0.0216 (331/15306). AF 95% confidence interval is 0.0197. There are 15 homozygotes in gnomad4. There are 699 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD1B | NM_001764.3 | c.310G>A | p.Gly104Ser | missense_variant | 2/6 | ENST00000368168.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD1B | ENST00000368168.4 | c.310G>A | p.Gly104Ser | missense_variant | 2/6 | 1 | NM_001764.3 | P1 | |
CD1B | ENST00000451207.5 | c.214G>A | p.Gly72Ser | missense_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00989 AC: 1505AN: 152162Hom.: 15 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00931 AC: 2333AN: 250508Hom.: 25 AF XY: 0.00946 AC XY: 1282AN XY: 135488
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GnomAD4 exome AF: 0.0128 AC: 18707AN: 1461724Hom.: 145 Cov.: 32 AF XY: 0.0125 AC XY: 9060AN XY: 727168
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GnomAD4 genome ? AF: 0.00987 AC: 1503AN: 152280Hom.: 15 Cov.: 32 AF XY: 0.00939 AC XY: 699AN XY: 74480
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58
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ESP6500AA
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133
ExAC
?
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1049
Asia WGS
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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 | Jan 11, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at