Variant 1-158181428-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001371762.2(CD1D):c.62-27A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 1,607,924 control chromosomes in the GnomAD database, including 19,489 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.12 ( 1635 hom., cov: 32)

Exomes 𝑓: 0.14 ( 17854 hom. )

Consequence

CD1D
NM_001371762.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Variant links:

Genes affected

CD1D (HGNC:1637): (CD1d molecule) This gene encodes a divergent 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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

CD1D links:

CD1D (HGNC:):

CD1D links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 2 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD1D	NM_001371762.2 linkuse as main transcript	c.62-27A>G		intron_variant		ENST00000674085.2	NP_001358691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD1D	ENST00000674085.2 linkuse as main transcript	c.62-27A>G		intron_variant			NM_001371762.2	ENSP00000501100.1		P15813

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18837

AN:

151966

Hom.:

1635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0835

Gnomad AMI

AF:

0.00661

Gnomad AMR

AF:

0.0973

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.167

AC:

41851

AN:

249994

Hom.:

5046

AF XY:

0.174

AC XY:

23525

AN XY:

135334

show subpopulations

Gnomad AFR exome

AF:

0.0867

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.163

Gnomad EAS exome

AF:

0.435

Gnomad SAS exome

AF:

0.336

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.110

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.139

AC:

202789

AN:

1455838

Hom.:

17854

Cov.:

AF XY:

0.144

AC XY:

104280

AN XY:

723020

show subpopulations

Gnomad4 AFR exome

AF:

0.0814

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.165

Gnomad4 EAS exome

AF:

0.380

Gnomad4 SAS exome

AF:

0.330

Gnomad4 FIN exome

AF:

0.122

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.124

AC:

18844

AN:

152086

Hom.:

1635

Cov.:

AF XY:

0.130

AC XY:

9672

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.0837

Gnomad4 AMR

AF:

0.0975

Gnomad4 ASJ

AF:

0.178

Gnomad4 EAS

AF:

0.435

Gnomad4 SAS

AF:

0.350

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.116

Hom.:

309

Bravo

AF:

0.117

Asia WGS

AF:

0.325

AC:

1129

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.2

DANN

Benign

0.34

La Branchor

0.82

BranchPoint Hunter

2.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over