Genetic Variant CXADR:p.Leu9Phe (chr21-17513154-C-T) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001338.5(CXADR):c.25C>T(p.Leu9Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CXADR
NM_001338.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0370

Publications

0 publications found

Variant links:

Genes affected

CXADR (HGNC:2559): (CXADR Ig-like cell adhesion molecule) The protein encoded by this gene is a type I membrane receptor for group B coxsackieviruses and subgroup C adenoviruses. Several transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene are found on chromosomes 15, 18, and 21. [provided by RefSeq, May 2011]

CXADR links:

ENSG00000304967 (HGNC:):

ENSG00000304967 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.29527113).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001338.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CXADR	NM_001338.5	MANE Select	c.25C>T	p.Leu9Phe	missense	Exon 1 of 7	NP_001329.1	P78310-1
CXADR	NM_001207066.2		c.25C>T	p.Leu9Phe	missense	Exon 1 of 8	NP_001193995.1	P78310-6
CXADR	NM_001207063.2		c.25C>T	p.Leu9Phe	missense	Exon 1 of 5	NP_001193992.1	P78310-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CXADR	ENST00000284878.12	TSL:1 MANE Select	c.25C>T	p.Leu9Phe	missense	Exon 1 of 7	ENSP00000284878.7	P78310-1
CXADR	ENST00000400166.5	TSL:1	c.25C>T	p.Leu9Phe	missense	Exon 1 of 5	ENSP00000383030.1	P78310-5
CXADR	ENST00000400165.5	TSL:1	c.25C>T	p.Leu9Phe	missense	Exon 1 of 4	ENSP00000383029.1	P78310-4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1225240

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

596096

African (AFR)

AF:

0.00

AC:

AN:

24312

American (AMR)

AF:

0.00

AC:

AN:

11514

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17432

East Asian (EAS)

AF:

0.00

AC:

AN:

28088

South Asian (SAS)

AF:

0.00

AC:

AN:

49742

European-Finnish (FIN)

AF:

0.00

AC:

AN:

44956

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4708

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

995140

Other (OTH)

AF:

0.00

AC:

AN:

49348

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.026

BayesDel_noAF

Benign

-0.27

CADD

Benign

(source)

DANN

Benign

0.85

DEOGEN2

Benign

0.24

Eigen

Benign

-0.93

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.032

LIST_S2

Benign

0.65

M_CAP

Pathogenic

0.97

MetaRNN

Benign

0.30

MetaSVM

Benign

-0.51

MutationAssessor

Benign

0.98

PhyloP100

0.037

PrimateAI

Uncertain

0.69

PROVEAN

Benign

-0.38

REVEL

Benign

0.22

Sift

Benign

0.14

Sift4G

Benign

0.13

Polyphen

0.015

Vest4

0.069

MutPred

0.46

Gain of sheet (P = 0.0149)

MVP

0.74

MPC

0.33

ClinPred

0.078

GERP RS

1.1

PromoterAI

0.13

Neutral

(source)

Varity_R

0.086

gMVP

0.35

Mutation Taster

=79/21

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over