Genetic Variant C1QTNF6:c.-70-2837G>A (chr22-37193765-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001365878.1(C1QTNF6):c.-70-2837G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,078 control chromosomes in the GnomAD database, including 2,686 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 0.18 ( 2686 hom., cov: 33)

Consequence

C1QTNF6
NM_001365878.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.762

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
C1QTNF6	NM_001365878.1 link	c.-70-2837G>A	intron_variant	Intron 2 of 4	NP_001352807.1
C1QTNF6	XM_024452150.2 link	c.-190+1616G>A	intron_variant	Intron 2 of 5	XP_024307918.1
C1QTNF6	XM_024452153.2 link	c.-190+1616G>A	intron_variant	Intron 2 of 5	XP_024307921.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C1QTNF6	ENST00000467564.5 link	n.224+1616G>A	intron_variant	Intron 2 of 4	3
C1QTNF6	ENST00000470655.5 link	n.2921+1616G>A	intron_variant	Intron 1 of 8	2
C1QTNF6	ENST00000497071.1 link	n.433+1616G>A	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27448

AN:

151958

Hom.:

2689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.177

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.180

AC:

27432

AN:

152078

Hom.:

2686

Cov.:

AF XY:

0.176

AC XY:

13116

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.183

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.229

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.208

Hom.:

4551

Bravo

AF:

0.170

Asia WGS

AF:

0.130

AC:

452

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

0.42

DANN

Benign

0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over