dbSNP rs7663443: C1QTNF7-AS1:n.87-43606A>G (chr4-15307070-T-C) – 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.87-43606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,290 control chromosomes in the GnomAD database, including 873 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 0.067 ( 873 hom., cov: 33)

Consequence

C1QTNF7-AS1
ENST00000502344.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.246

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF7-AS1	NR_125911.1 link	n.87-43606A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C1QTNF7-AS1	ENST00000502344.6 link	n.87-43606A>G	intron_variant	Intron 1 of 5	3
C1QTNF7-AS1	ENST00000803075.1 link	n.88-7414A>G	intron_variant	Intron 1 of 1
C1QTNF7-AS1	ENST00000803076.1 link	n.191-7414A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0673

AC:

10239

AN:

152172

Hom.:

875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0289

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0553

Gnomad FIN

AF:

0.00781

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0132

Gnomad OTH

AF:

0.0501

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

GnomAD4 genome

AF:

0.0673

AC:

10249

AN:

152290

Hom.:

873

Cov.:

AF XY:

0.0652

AC XY:

4855

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.202

AC:

8380

AN:

41532

American (AMR)

AF:

0.0289

AC:

442

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0112

AC:

AN:

3472

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0555

AC:

268

AN:

4826

European-Finnish (FIN)

AF:

0.00781

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0132

AC:

901

AN:

68028

Other (OTH)

AF:

0.0506

AC:

107

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

429

859

1288

1718

2147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0224

Hom.:

200

Bravo

AF:

0.0739

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.0

(source)

DANN

Benign

0.49

PhyloP100

0.25

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