Genetic Variant C1QTNF7-AS1:n.87-21534T>C (chr4-15284998-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000502344.6(C1QTNF7-AS1):n.87-21534T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 150,870 control chromosomes in the GnomAD database, including 38,403 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 0.70 ( 38403 hom., cov: 32)

Consequence

C1QTNF7-AS1
ENST00000502344.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06

Publications

1 publications found

Variant links:

Genes affected

C1QTNF7-AS1 (HGNC:40683): (C1QTNF7 antisense RNA 1)

C1QTNF7-AS1 links:

Genome browser will be placed here

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 = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF7-AS1	NR_125911.1 link	n.87-21534T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.6 link	n.87-21534T>C		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

105928

AN:

150788

Hom.:

38345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.843

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.995

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.725

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.660

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

GnomAD4 genome

AF:

0.703

AC:

106028

AN:

150870

Hom.:

38403

Cov.:

AF XY:

0.710

AC XY:

52351

AN XY:

73718

show subpopulations

African (AFR)

AF:

0.844

AC:

34861

AN:

41322

American (AMR)

AF:

0.702

AC:

10639

AN:

15166

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

2037

AN:

3464

East Asian (EAS)

AF:

0.995

AC:

5135

AN:

5162

South Asian (SAS)

AF:

0.747

AC:

3583

AN:

4796

European-Finnish (FIN)

AF:

0.725

AC:

7260

AN:

10014

Middle Eastern (MID)

AF:

0.486

AC:

139

AN:

286

European-Non Finnish (NFE)

AF:

0.596

AC:

40320

AN:

67650

Other (OTH)

AF:

0.663

AC:

1392

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1483

2966

4450

5933

7416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.678

Hom.:

4609

Bravo

AF:

0.708

Asia WGS

AF:

0.868

AC:

2936

AN:

3386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.69

(source)

DANN

Benign

0.29

PhyloP100

-2.1

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