Genetic Variant NM_001365878.1:c.-71+2325C>T (chr22-37195278-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_001365878.1(C1QTNF6):c.-71+2325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,102 control chromosomes in the GnomAD database, including 19,317 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 0.49 ( 19316 hom., cov: 33)

Exomes 𝑓: 0.63 ( 1 hom. )

Consequence

C1QTNF6
NM_001365878.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

Publications

81 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:

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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=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
C1QTNF6	NM_001365878.1 link	c.-71+2325C>T	intron_variant	Intron 2 of 4	NP_001352807.1
C1QTNF6	XM_024452150.2 link	c.-190+103C>T	intron_variant	Intron 2 of 5	XP_024307918.1
C1QTNF6	XM_024452153.2 link	c.-190+103C>T	intron_variant	Intron 2 of 5	XP_024307921.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C1QTNF6	ENST00000467564.5 link	n.224+103C>T	intron_variant	Intron 2 of 4	3
C1QTNF6	ENST00000470655.5 link	n.2921+103C>T	intron_variant	Intron 1 of 8	2
C1QTNF6	ENST00000497071.1 link	n.433+103C>T	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.494

AC:

75077

AN:

151976

Hom.:

19288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.628

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.686

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.497

GnomAD4 exome

AF:

0.625

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.494

AC:

75147

AN:

152094

Hom.:

19316

Cov.:

AF XY:

0.493

AC XY:

36636

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.628

AC:

26057

AN:

41474

American (AMR)

AF:

0.455

AC:

6953

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

1791

AN:

3466

East Asian (EAS)

AF:

0.687

AC:

3553

AN:

5174

South Asian (SAS)

AF:

0.454

AC:

2187

AN:

4818

European-Finnish (FIN)

AF:

0.386

AC:

4085

AN:

10574

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.426

AC:

28946

AN:

67986

Other (OTH)

AF:

0.495

AC:

1047

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1884

3769

5653

7538

9422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.454

Hom.:

54665

Bravo

AF:

0.511

Asia WGS

AF:

0.558

AC:

1938

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.44

(source)

DANN

Benign

0.40

PhyloP100

-2.0

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over