1-158325839-A-G

Position:

• chr1-158325839-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CD1B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD1B	XM_017002784.3	c.607+4013T>C		intron_variant
CD1B	XM_017002785.3	c.607+4013T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.454

Alfa AF: 0.381 Hom.: 23535

Bravo AF: 0.509

Asia WGS AF: 0.624 AC: 2167 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10797007; hg19: chr1-158295629;