Variant chr1-117011799-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001256106.3(CD101):c.674A>G(p.Asn225Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,613,850 control chromosomes in the GnomAD database, including 71,147 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.23 ( 4988 hom., cov: 32)

Exomes 𝑓: 0.29 ( 66159 hom. )

Consequence

CD101
NM_001256106.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.905

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013926327).

BP6

Variant 1-117011799-A-G is Benign according to our data. Variant chr1-117011799-A-G is described in ClinVar as [Benign]. Clinvar id is 1280460.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD101	NM_001256106.3 linkuse as main transcript	c.674A>G	p.Asn225Ser	missense_variant	3/10	ENST00000682167.1	NP_001243035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CD101	ENST00000682167.1 linkuse as main transcript	c.674A>G	p.Asn225Ser	missense_variant	3/10		NM_001256106.3	ENSP00000508039	P1
CD101	ENST00000369470.1 linkuse as main transcript	c.674A>G	p.Asn225Ser	missense_variant	3/10	1		ENSP00000358482	P1
CD101	ENST00000256652.8 linkuse as main transcript	c.674A>G	p.Asn225Ser	missense_variant	3/9	2		ENSP00000256652	P1

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

35033

AN:

152012

Hom.:

4988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0802

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.0697

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.258

GnomAD3 exomes

AF:

0.249

AC:

62534

AN:

250790

Hom.:

9060

AF XY:

0.255

AC XY:

34510

AN XY:

135528

show subpopulations

Gnomad AFR exome

AF:

0.0704

Gnomad AMR exome

AF:

0.160

Gnomad ASJ exome

AF:

0.435

Gnomad EAS exome

AF:

0.0760

Gnomad SAS exome

AF:

0.176

Gnomad FIN exome

AF:

0.292

Gnomad NFE exome

AF:

0.323

Gnomad OTH exome

AF:

0.290

GnomAD4 exome

AF:

0.293

AC:

427730

AN:

1461720

Hom.:

66159

Cov.:

AF XY:

0.291

AC XY:

211668

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.0702

Gnomad4 AMR exome

AF:

0.168

Gnomad4 ASJ exome

AF:

0.436

Gnomad4 EAS exome

AF:

0.0812

Gnomad4 SAS exome

AF:

0.180

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.318

Gnomad4 OTH exome

AF:

0.276

GnomAD4 genome

AF:

0.230

AC:

35020

AN:

152130

Hom.:

4988

Cov.:

AF XY:

0.226

AC XY:

16790

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0799

Gnomad4 AMR

AF:

0.222

Gnomad4 ASJ

AF:

0.437

Gnomad4 EAS

AF:

0.0698

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.320

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.302

Hom.:

14952

Bravo

AF:

0.221

TwinsUK

AF:

0.315

AC:

1169

ALSPAC

AF:

0.306

AC:

1178

ESP6500AA

AF:

0.0890

AC:

392

ESP6500EA

AF:

0.325

AC:

2794

ExAC

AF:

0.248

AC:

30141

EpiCase

AF:

0.325

EpiControl

AF:

0.326

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 23, 2021	This variant is associated with the following publications: (PMID: 29108000) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.30

DANN

Benign

0.83

DEOGEN2

Benign

0.13

T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.0

FATHMM_MKL

Uncertain

0.84

LIST_S2

Benign

0.64

T;.

MetaRNN

Benign

0.0014

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.38

N;N

MutationTaster

Benign

0.99

P;P

PrimateAI

Benign

0.23

PROVEAN

Benign

-1.0

N;N

REVEL

Benign

0.059

Sift

Benign

0.054

T;T

Sift4G

Benign

0.099

T;T

Polyphen

0.0

B;B

Vest4

0.012

MPC

0.075

ClinPred

0.0074

GERP RS

-2.3

Varity_R

0.045

gMVP

0.079

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over