Genetic Variant ADCY7:c.*794G>A (chr16-50316299-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_001114.5(ADCY7):c.*794G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,290 control chromosomes in the GnomAD database, including 6,407 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 0.27 ( 6405 hom., cov: 33)

Exomes 𝑓: 0.18 ( 2 hom. )

Consequence

ADCY7
NM_001114.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291

Publications

17 publications found

Variant links:

Genes affected

ADCY7 (HGNC:238): (adenylate cyclase 7) This gene encodes a membrane-bound adenylate cyclase that catalyses the formation of cyclic AMP from ATP and is inhibitable by calcium. The product of this gene is a member of the adenylyl cyclase class-4/guanylyl cyclase enzyme family that is characterized by the presence of twelve membrane-spanning domains in its sequences. Several transcript variants have been observed for this gene, but the full-length natures of only two have been determined so far. [provided by RefSeq, Oct 2013]

ADCY7 links:

BRD7 (HGNC:14310): (bromodomain containing 7) This gene encodes a protein which is a member of the bromodomain-containing protein family. The product of this gene has been identified as a component of one form of the SWI/SNF chromatin remodeling complex, and as a protein which interacts with p53 and is required for p53-dependent oncogene-induced senescence which prevents tumor growth. Pseudogenes have been described on chromosomes 2, 3, 6, 13 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

BRD7 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADCY7	NM_001114.5	MANE Select	c.*794G>A	3_prime_UTR	Exon 26 of 26	NP_001105.1
BRD7	NM_013263.5	MANE Select	c.*2912C>T	3_prime_UTR	Exon 17 of 17	NP_037395.2
BRD7	NM_001438173.1		c.*2912C>T	3_prime_UTR	Exon 17 of 17	NP_001425102.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADCY7	ENST00000673801.1	MANE Select	c.*794G>A	3_prime_UTR	Exon 26 of 26	ENSP00000501053.1
BRD7	ENST00000394688.8	TSL:1 MANE Select	c.*2912C>T	3_prime_UTR	Exon 17 of 17	ENSP00000378180.3
ADCY7	ENST00000254235.7	TSL:1	c.*794G>A	3_prime_UTR	Exon 25 of 25	ENSP00000254235.3

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40942

AN:

151974

Hom.:

6393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.426

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.238

GnomAD4 exome

AF:

0.182

AC:

AN:

198

Hom.:

Cov.:

AF XY:

0.153

AC XY:

AN XY:

118

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.194

AC:

AN:

134

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.152

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.270

AC:

40999

AN:

152092

Hom.:

6405

Cov.:

AF XY:

0.270

AC XY:

20058

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.427

AC:

17675

AN:

41434

American (AMR)

AF:

0.320

AC:

4898

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

746

AN:

3472

East Asian (EAS)

AF:

0.301

AC:

1557

AN:

5172

South Asian (SAS)

AF:

0.264

AC:

1272

AN:

4824

European-Finnish (FIN)

AF:

0.154

AC:

1635

AN:

10594

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.183

AC:

12458

AN:

67990

Other (OTH)

AF:

0.241

AC:

508

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1450

2899

4349

5798

7248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.214

Hom.:

5046

Bravo

AF:

0.287

Asia WGS

AF:

0.288

AC:

1001

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.76

(source)

DANN

Benign

0.31

PhyloP100

-0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over