Genetic Variant CNBD1:c.1372-9102G>C (chr8-87462146-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000523299.6(CNBD1):c.1372-9102G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,940 control chromosomes in the GnomAD database, including 11,641 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 0.38 ( 11641 hom., cov: 31)

Consequence

CNBD1
ENST00000523299.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106

Publications

1 publications found

Variant links:

Genes affected

CNBD1 (HGNC:26663): (cyclic nucleotide binding domain containing 1)

CNBD1 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=-0.97).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000523299.6 link	c.1372-9102G>C		intron_variant	Intron 11 of 12	3		ENSP00000430986.2		H0YC59
CNBD1	ENST00000521593.5 link	c.280-9102G>C		intron_variant	Intron 3 of 7	3		ENSP00000427742.1		H0YAN5

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58147

AN:

151824

Hom.:

11642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.393

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

GnomAD4 genome

AF:

0.383

AC:

58153

AN:

151940

Hom.:

11641

Cov.:

AF XY:

0.382

AC XY:

28394

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.272

AC:

11265

AN:

41452

American (AMR)

AF:

0.472

AC:

7201

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

1747

AN:

3470

East Asian (EAS)

AF:

0.344

AC:

1775

AN:

5160

South Asian (SAS)

AF:

0.367

AC:

1768

AN:

4820

European-Finnish (FIN)

AF:

0.400

AC:

4215

AN:

10538

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.425

AC:

28902

AN:

67934

Other (OTH)

AF:

0.388

AC:

818

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1808

3616

5425

7233

9041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.397

Hom.:

1539

Bravo

AF:

0.384

Asia WGS

AF:

0.351

AC:

1220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.0

(source)

DANN

Benign

0.46

PhyloP100

-0.11

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