chr1-158286506-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The XM_017002785.3(CD1B):​c.*1421A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 152,306 control chromosomes in the GnomAD database, including 123 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 0.035 ( 123 hom., cov: 32)

Consequence

CD1B
XM_017002785.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.557

Publications

6 publications found
Variant links:
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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0347 (5279/152306) while in subpopulation EAS AF = 0.0524 (271/5170). AF 95% confidence interval is 0.0473. There are 123 homozygotes in GnomAd4. There are 2645 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 123 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD1BXM_017002785.3 linkc.*1421A>G 3_prime_UTR_variant Exon 4 of 4 XP_016858274.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0347
AC:
5278
AN:
152188
Hom.:
123
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00900
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.0272
Gnomad ASJ
AF:
0.0334
Gnomad EAS
AF:
0.0527
Gnomad SAS
AF:
0.0372
Gnomad FIN
AF:
0.0762
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0441
Gnomad OTH
AF:
0.0425
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0347
AC:
5279
AN:
152306
Hom.:
123
Cov.:
32
AF XY:
0.0355
AC XY:
2645
AN XY:
74480
show subpopulations
African (AFR)
AF:
0.00907
AC:
377
AN:
41580
American (AMR)
AF:
0.0271
AC:
414
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.0334
AC:
116
AN:
3472
East Asian (EAS)
AF:
0.0524
AC:
271
AN:
5170
South Asian (SAS)
AF:
0.0375
AC:
181
AN:
4830
European-Finnish (FIN)
AF:
0.0762
AC:
809
AN:
10612
Middle Eastern (MID)
AF:
0.0102
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
0.0441
AC:
2999
AN:
68026
Other (OTH)
AF:
0.0421
AC:
89
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
275
550
824
1099
1374
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
66
132
198
264
330
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0368
Hom.:
292
Bravo
AF:
0.0305
Asia WGS
AF:
0.0340
AC:
118
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.1
DANN
Benign
0.43
PhyloP100
0.56

Splicing

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

Publications

Other links and lift over

dbSNP: rs12033535; hg19: chr1-158256296; API