1-117024426-A-G

Position:

• chr1-117024426-A-G

Variant summary

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

The NM_001256106.3(CD101):​c.2429-1083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,026 control chromosomes in the GnomAD database, including 11,479 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 0.38 (11479 hom., cov: 33)
• Consequence: CD101 NM_001256106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57

Genes affected

CD101 (HGNC:5949): (CD101 molecule) Predicted to enable hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides. Predicted to be involved in cell surface receptor signaling pathway. Predicted to act upstream of or within positive regulation of myeloid leukocyte differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD101	NM_001256106.3	c.2429-1083A>G		intron_variant		ENST00000682167.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD101	ENST00000682167.1	c.2429-1083A>G		intron_variant			NM_001256106.3	P1
CD101	ENST00000369470.1	c.2429-1083A>G		intron_variant		1		P1
CD101	ENST00000256652.8	c.2429-1083A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57684 AN: 151908 Hom.: 11445 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.380 AC: 57753 AN: 152026 Hom.: 11479 Cov.: 33 AF XY: 0.391 AC XY: 29058 AN XY: 74338

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.365

Alfa AF: 0.251 Hom.: 612

Bravo AF: 0.381

Asia WGS AF: 0.541 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs4659344; hg19: chr1-117567048;