1-117009362-G-A

Position:

• chr1-117009362-G-A

Variant summary

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

The NM_001256106.3(CD101):​c.44-488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,114 control chromosomes in the GnomAD database, including 12,638 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 0.40 (12638 hom., cov: 33)
• Consequence: CD101 NM_001256106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD101	NM_001256106.3	c.44-488G>A		intron_variant		ENST00000682167.1	NP_001243035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD101	ENST00000682167.1	c.44-488G>A		intron_variant			NM_001256106.3	ENSP00000508039	P1
CD101	ENST00000369470.1	c.44-488G>A		intron_variant		1		ENSP00000358482	P1
CD101	ENST00000256652.8	c.44-488G>A		intron_variant		2		ENSP00000256652	P1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60856 AN: 151996 Hom.: 12601 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.401 AC: 60939 AN: 152114 Hom.: 12638 Cov.: 33 AF XY: 0.412 AC XY: 30603 AN XY: 74340

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.397

Alfa AF: 0.389 Hom.: 1670

Bravo AF: 0.404

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.92
DANN	Benign	0.35

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: rs9332416; hg19: chr1-117551984;