Genetic Variant C1QTNF6:c.52-671G>A (chr22-37186126-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031910.4(C1QTNF6):c.52-671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 985,184 control chromosomes in the GnomAD database, including 20,711 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 0.23 ( 4270 hom., cov: 33)

Exomes 𝑓: 0.20 ( 16441 hom. )

Consequence

C1QTNF6
NM_031910.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13

Publications

7 publications found

Variant links:

Genes affected

C1QTNF6 (HGNC:14343): (C1q and TNF related 6) Predicted to enable identical protein binding activity. Predicted to be located in extracellular space. Predicted to be integral component of membrane. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

C1QTNF6 links:

IL2RB-AS1 (HGNC:40300):

IL2RB-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF6	NM_031910.4 link	c.52-671G>A		intron_variant	Intron 1 of 2	ENST00000337843.7	NP_114116.3	Q9BXI9-2A0A024R1J0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF6	ENST00000337843.7 link	c.52-671G>A		intron_variant	Intron 1 of 2	1	NM_031910.4	ENSP00000338812.2		Q9BXI9-2

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34293

AN:

152080

Hom.:

4266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.580

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.196

Gnomad OTH

AF:

0.258

GnomAD4 exome

AF:

0.195

AC:

162825

AN:

832986

Hom.:

16441

AF XY:

0.195

AC XY:

75053

AN XY:

384690

show subpopulations

African (AFR)

AF:

0.202

AC:

3191

AN:

15782

American (AMR)

AF:

0.303

AC:

298

AN:

982

Ashkenazi Jewish (ASJ)

AF:

0.305

AC:

1572

AN:

5152

East Asian (EAS)

AF:

0.574

AC:

2083

AN:

3632

South Asian (SAS)

AF:

0.260

AC:

4282

AN:

16454

European-Finnish (FIN)

AF:

0.177

AC:

AN:

288

Middle Eastern (MID)

AF:

0.275

AC:

445

AN:

1620

European-Non Finnish (NFE)

AF:

0.190

AC:

144373

AN:

761778

Other (OTH)

AF:

0.239

AC:

6530

AN:

27298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

6847

13694

20542

27389

34236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7042

14084

21126

28168

35210

<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:

0.225

AC:

34319

AN:

152198

Hom.:

4270

Cov.:

AF XY:

0.230

AC XY:

17141

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.200

AC:

8308

AN:

41530

American (AMR)

AF:

0.292

AC:

4458

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1083

AN:

3470

East Asian (EAS)

AF:

0.581

AC:

3008

AN:

5176

South Asian (SAS)

AF:

0.268

AC:

1294

AN:

4826

European-Finnish (FIN)

AF:

0.188

AC:

1990

AN:

10596

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.196

AC:

13295

AN:

68000

Other (OTH)

AF:

0.258

AC:

543

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1378

2756

4134

5512

6890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.146

Hom.:

313

Bravo

AF:

0.239

Asia WGS

AF:

0.400

AC:

1390

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.011

(source)

DANN

Benign

0.52

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(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

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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