Genetic Variant C1QTNF9:p.Val130Met (chr13-24321154-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_178540.5(C1QTNF9):c.388G>A(p.Val130Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000027 in 1,368,964 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00015 ( 1 hom., cov: 15)

Exomes 𝑓: 0.000017 ( 0 hom. )

Consequence

C1QTNF9
NM_178540.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.89

Publications

0 publications found

Variant links:

Genes affected

C1QTNF9 (HGNC:28732): (C1q and TNF related 9) Enables identical protein binding activity. Predicted to be involved in signal transduction. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

C1QTNF9 links:

PCOTHP1 (HGNC:39840):

PCOTHP1 links:

C1QTNF9-AS1 (HGNC:39906): (C1QTNF9 antisense RNA 1)

C1QTNF9-AS1 links:

ENSG00000273167 (HGNC:):

ENSG00000273167 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.1731494).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178540.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C1QTNF9	NM_178540.5	MANE Select	c.388G>A	p.Val130Met	missense	Exon 4 of 4	NP_848635.2	P0C862
C1QTNF9	NM_001303137.2		c.388G>A	p.Val130Met	missense	Exon 5 of 5	NP_001290066.1	P0C862
C1QTNF9	NM_001303138.2		c.388G>A	p.Val130Met	missense	Exon 4 of 4	NP_001290067.1	P0C862

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C1QTNF9	ENST00000332018.5	TSL:1 MANE Select	c.388G>A	p.Val130Met	missense	Exon 4 of 4	ENSP00000333737.4	P0C862
C1QTNF9	ENST00000382071.6	TSL:5	c.388G>A	p.Val130Met	missense	Exon 4 of 4	ENSP00000371503.2	P0C862
C1QTNF9	ENST00000875261.1		c.388G>A	p.Val130Met	missense	Exon 5 of 5	ENSP00000545320.1

Frequencies

GnomAD3 genomes

AF:

0.000149

AC:

AN:

107716

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000441

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000212

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000394

AC:

AN:

126780

AF XY:

0.0000444

show subpopulations

Gnomad AFR exome

AF:

0.000346

Gnomad AMR exome

AF:

0.0000514

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000167

AC:

AN:

1261248

Hom.:

Cov.:

AF XY:

0.0000192

AC XY:

AN XY:

624524

show subpopulations

African (AFR)

AF:

0.000129

AC:

AN:

31042

American (AMR)

AF:

0.0000327

AC:

AN:

30568

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21088

East Asian (EAS)

AF:

0.00

AC:

AN:

37080

South Asian (SAS)

AF:

0.0000276

AC:

AN:

72586

European-Finnish (FIN)

AF:

0.00

AC:

AN:

41270

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4426

European-Non Finnish (NFE)

AF:

0.0000124

AC:

AN:

970152

Other (OTH)

AF:

0.0000377

AC:

AN:

53036

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.587

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.000149

AC:

AN:

107716

Hom.:

Cov.:

AF XY:

0.000178

AC XY:

AN XY:

50518

show subpopulations

African (AFR)

AF:

0.000441

AC:

AN:

34010

American (AMR)

AF:

0.00

AC:

AN:

10018

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2512

East Asian (EAS)

AF:

0.00

AC:

AN:

4016

South Asian (SAS)

AF:

0.00

AC:

AN:

3380

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4354

Middle Eastern (MID)

AF:

0.00

AC:

AN:

250

European-Non Finnish (NFE)

AF:

0.0000212

AC:

AN:

47090

Other (OTH)

AF:

0.00

AC:

AN:

1454

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.621

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000356

Hom.:

Bravo

AF:

0.000147

ExAC

AF:

0.0000679

AC:

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

0.080

BayesDel_addAF

Benign

0.0030

BayesDel_noAF

Benign

-0.22

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.17

Eigen

Benign

0.14

Eigen_PC

Benign

0.085

FATHMM_MKL

Uncertain

0.79

LIST_S2

Benign

0.76

M_CAP

Uncertain

0.19

MetaRNN

Benign

0.17

MetaSVM

Uncertain

-0.20

MutationAssessor

Benign

0.27

PhyloP100

2.9

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-0.44

REVEL

Uncertain

0.32

Sift

Benign

0.20

Sift4G

Benign

0.11

Polyphen

0.98

Vest4

0.091

MVP

0.84

ClinPred

0.068

GERP RS

4.0

Varity_R

0.054

gMVP

0.28

Mutation Taster

=99/1

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over