Genetic Variant NM_031910.4:c.290-185C>T (chr22-37182920-G-A) – 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.290-185C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 1,429,598 control chromosomes in the GnomAD database, including 68,274 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 0.39 ( 12982 hom., cov: 33)

Exomes 𝑓: 0.28 ( 55292 hom. )

Consequence

C1QTNF6
NM_031910.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.864

Publications

9 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031910.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1QTNF6	NM_031910.4	MANE Select	c.290-185C>T	intron	N/A	NP_114116.3
C1QTNF6	NM_182486.2		c.290-185C>T	intron	N/A	NP_872292.1	Q9BXI9-2
C1QTNF6	NM_001365878.1		c.233-185C>T	intron	N/A	NP_001352807.1	Q9BXI9-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1QTNF6	ENST00000337843.7	TSL:1 MANE Select	c.290-185C>T	intron	N/A	ENSP00000338812.2	Q9BXI9-2
C1QTNF6	ENST00000397110.6	TSL:1	c.290-185C>T	intron	N/A	ENSP00000380299.2	Q9BXI9-2
C1QTNF6	ENST00000493023.1	TSL:1	n.732-185C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58636

AN:

151994

Hom.:

12920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.591

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.434

Gnomad ASJ

AF:

0.366

Gnomad EAS

AF:

0.491

Gnomad SAS

AF:

0.374

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.284

AC:

362599

AN:

1277486

Hom.:

55292

Cov.:

AF XY:

0.286

AC XY:

176573

AN XY:

618420

show subpopulations

African (AFR)

AF:

0.610

AC:

17173

AN:

28154

American (AMR)

AF:

0.465

AC:

8744

AN:

18796

Ashkenazi Jewish (ASJ)

AF:

0.353

AC:

6634

AN:

18804

East Asian (EAS)

AF:

0.469

AC:

16216

AN:

34554

South Asian (SAS)

AF:

0.380

AC:

22920

AN:

60270

European-Finnish (FIN)

AF:

0.276

AC:

8273

AN:

30022

Middle Eastern (MID)

AF:

0.400

AC:

1928

AN:

4824

European-Non Finnish (NFE)

AF:

0.256

AC:

262975

AN:

1028828

Other (OTH)

AF:

0.333

AC:

17736

AN:

53234

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

12435

24870

37306

49741

62176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9584

19168

28752

38336

47920

<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:

0.386

AC:

58775

AN:

152112

Hom.:

12982

Cov.:

AF XY:

0.388

AC XY:

28856

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.592

AC:

24556

AN:

41494

American (AMR)

AF:

0.435

AC:

6658

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.366

AC:

1269

AN:

3468

East Asian (EAS)

AF:

0.492

AC:

2541

AN:

5164

South Asian (SAS)

AF:

0.376

AC:

1816

AN:

4828

European-Finnish (FIN)

AF:

0.260

AC:

2754

AN:

10590

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

17980

AN:

67952

Other (OTH)

AF:

0.396

AC:

838

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1736

3471

5207

6942

8678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.318

Hom.:

4915

Bravo

AF:

0.412

Asia WGS

AF:

0.469

AC:

1632

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.89

(source)

DANN

Benign

0.47

PhyloP100

-0.86

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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