1-158312109-A-T

Position:

• chr1-158312109-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017002784.3(CD1B):​c.608-17071T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,972 control chromosomes in the GnomAD database, including 8,203 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 0.32 (8203 hom., cov: 32)
• Consequence: CD1B XM_017002784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

CD1B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD1B	XM_017002784.3	c.608-17071T>A		intron_variant			XP_016858273.1
CD1B	XM_017002785.3	c.607+17743T>A		intron_variant			XP_016858274.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48224 AN: 151854 Hom.: 8186 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.318 AC: 48287 AN: 151972 Hom.: 8203 Cov.: 32 AF XY: 0.322 AC XY: 23917 AN XY: 74262

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.313

Alfa AF: 0.160 Hom.: 293

Bravo AF: 0.325

Asia WGS AF: 0.385 AC: 1336 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	4.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1590230; hg19: chr1-158281899;