XM_017002784.3:c.607+4013T>C

Variant names:

• chr1-158325839-A-G
• rs10797007
• XM_017002784.3:c.607+4013T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017002784.3(CD1B):​c.607+4013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,102 control chromosomes in the GnomAD database, including 21,782 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 0.50 (21782 hom., cov: 33)
• Consequence: CD1B XM_017002784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 7 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76390 AN: 151984 Hom.: 21744 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.452

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.503 AC: 76489 AN: 152102 Hom.: 21782 Cov.: 33 AF XY: 0.506 AC XY: 37586 AN XY: 74338

African (AFR) AF: 0.771 AC: 31976 AN: 41482

American (AMR) AF: 0.434 AC: 6627 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3468

East Asian (EAS) AF: 0.658 AC: 3413 AN: 5186

South Asian (SAS) AF: 0.578 AC: 2785 AN: 4822

European-Finnish (FIN) AF: 0.398 AC: 4199 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24524 AN: 68000

Other (OTH) AF: 0.454 AC: 957 AN: 2110

Alfa AF: 0.401 Hom.: 59020

Bravo AF: 0.509

Asia WGS AF: 0.624 AC: 2167 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.58
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10797007; hg19: chr1-158295629;