Genetic Variant NM_001256106.3:c.-109A>C (chr1-117001709-A-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

11 publications found

Variant links:

COSMIC-nc: COSV56718118

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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

African (AFR)

AF:

0.00946

AC:

218

AN:

23044

American (AMR)

AF:

0.0161

AC:

566

AN:

35178

Ashkenazi Jewish (ASJ)

AF:

0.0271

AC:

564

AN:

20808

East Asian (EAS)

AF:

0.0000815

AC:

AN:

36814

South Asian (SAS)

AF:

0.00712

AC:

502

AN:

70498

European-Finnish (FIN)

AF:

0.100

AC:

4879

AN:

48602

Middle Eastern (MID)

AF:

0.00662

AC:

AN:

4686

European-Non Finnish (NFE)

AF:

0.0715

AC:

49690

AN:

694690

Other (OTH)

AF:

0.0515

AC:

2263

AN:

43976

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2740

5480

8220

10960

13700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1378

2756

4134

5512

6890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0490

AC:

7467

AN:

152266

Hom.:

266

Cov.:

AF XY:

0.0493

AC XY:

3671

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.0118

AC:

491

AN:

41562

American (AMR)

AF:

0.0278

AC:

425

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0285

AC:

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5182

South Asian (SAS)

AF:

0.00477

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0997

AC:

1058

AN:

10608

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0773

AC:

5258

AN:

68010

Other (OTH)

AF:

0.0331

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

371

742

1113

1484

1855

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0626

Hom.:

243

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

(source)

DANN

Benign

0.87

PhyloP100

2.6

PromoterAI

-0.042

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over