dbSNP rs12130298: CD101:c.-109A>C (chr1-117001709-A-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001256106.3(CD101):c.-109A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0585 in 1,130,562 control chromosomes in the GnomAD database, including 2,405 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 0.049 ( 266 hom., cov: 32)

Exomes 𝑓: 0.060 ( 2139 hom. )

Consequence

CD101
NM_001256106.3 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.58

Variant links:

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]

CD101 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD101	NM_001256106.3 link	c.-109A>C		upstream_gene_variant		ENST00000682167.1	NP_001243035.1	Q93033

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CD101	ENST00000682167.1 link	c.-109A>C	upstream_gene_variant		NM_001256106.3	ENSP00000508039.1	Q93033
CD101	ENST00000369470.1 link	c.-109A>C	upstream_gene_variant	1		ENSP00000358482.1	Q93033
CD101	ENST00000256652.8 link	c.-109A>C	upstream_gene_variant	2		ENSP00000256652.4	Q93033

Frequencies

GnomAD3 genomes

AF:

0.0491

AC:

7467

AN:

152148

Hom.:

266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0278

Gnomad ASJ

AF:

0.0285

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00477

Gnomad FIN

AF:

0.0997

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0773

Gnomad OTH

AF:

0.0334

GnomAD4 exome

AF:

0.0600

AC:

58716

AN:

978296

Hom.:

2139

Cov.:

AF XY:

0.0590

AC XY:

29763

AN XY:

504128

show subpopulations

Gnomad4 AFR exome

AF:

0.00946

Gnomad4 AMR exome

AF:

0.0161

Gnomad4 ASJ exome

AF:

0.0271

Gnomad4 EAS exome

AF:

0.0000815

Gnomad4 SAS exome

AF:

0.00712

Gnomad4 FIN exome

AF:

0.100

Gnomad4 NFE exome

AF:

0.0715

Gnomad4 OTH exome

AF:

0.0515

GnomAD4 genome

AF:

0.0490

AC:

7467

AN:

152266

Hom.:

266

Cov.:

AF XY:

0.0493

AC XY:

3671

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0118

Gnomad4 AMR

AF:

0.0278

Gnomad4 ASJ

AF:

0.0285

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00477

Gnomad4 FIN

AF:

0.0997

Gnomad4 NFE

AF:

0.0773

Gnomad4 OTH

AF:

0.0331

Alfa

AF:

0.0655

Hom.:

185

Bravo

AF:

0.0401

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.87

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over