Genetic Variant NM_001114.5:c.*1467T>G (chr16-50316972-T-G) – 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.*1467T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,646 control chromosomes in the GnomAD database, including 12,720 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 ( 12656 hom., cov: 32)

Exomes 𝑓: 0.46 ( 64 hom. )

Consequence

ADCY7
NM_001114.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.259

Publications

20 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY7	NM_001114.5 link	c.*1467T>G		3_prime_UTR_variant	Exon 26 of 26	ENST00000673801.1	NP_001105.1	P51828Q86YI0
BRD7	NM_013263.5 link	c.*2239A>C		3_prime_UTR_variant	Exon 17 of 17	ENST00000394688.8	NP_037395.2	Q9NPI1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY7	ENST00000673801.1 link	c.*1467T>G		3_prime_UTR_variant	Exon 26 of 26		NM_001114.5	ENSP00000501053.1		P51828
BRD7	ENST00000394688.8 link	c.*2239A>C		3_prime_UTR_variant	Exon 17 of 17	1	NM_013263.5	ENSP00000378180.3		Q9NPI1-1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57543

AN:

151954

Hom.:

12657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.428

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.419

GnomAD4 exome

AF:

0.458

AC:

263

AN:

574

Hom.:

Cov.:

AF XY:

0.455

AC XY:

153

AN XY:

336

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.493

AC:

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.446

AC:

183

AN:

410

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

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:

0.379

AC:

57570

AN:

152072

Hom.:

12656

Cov.:

AF XY:

0.376

AC XY:

27915

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.146

AC:

6070

AN:

41518

American (AMR)

AF:

0.418

AC:

6389

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1731

AN:

3472

East Asian (EAS)

AF:

0.210

AC:

1082

AN:

5164

South Asian (SAS)

AF:

0.430

AC:

2072

AN:

4818

European-Finnish (FIN)

AF:

0.447

AC:

4715

AN:

10556

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.500

AC:

33969

AN:

67954

Other (OTH)

AF:

0.419

AC:

884

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1684

3368

5052

6736

8420

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.459

Hom.:

19805

Bravo

AF:

0.368

Asia WGS

AF:

0.324

AC:

1128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.5

(source)

DANN

Benign

0.59

PhyloP100

0.26

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over