rs7191958

Variant names:

• chr16-50298262-A-G
• rs7191958
• NM_001114.5:c.949-642A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114.5(ADCY7):​c.949-642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,910 control chromosomes in the GnomAD database, including 34,157 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 0.66 (34157 hom., cov: 31)
• Consequence: ADCY7 NM_001114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 5 publications found

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]

ACMG classification

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 = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY7	NM_001114.5	c.949-642A>G		intron_variant	Intron 7 of 25	ENST00000673801.1	NP_001105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY7	ENST00000673801.1	c.949-642A>G		intron_variant	Intron 7 of 25		NM_001114.5	ENSP00000501053.1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100536 AN: 151790 Hom.: 34130 Cov.: 31

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.662 AC: 100612 AN: 151910 Hom.: 34157 Cov.: 31 AF XY: 0.650 AC XY: 48284 AN XY: 74246

African (AFR) AF: 0.709 AC: 29380 AN: 41440

American (AMR) AF: 0.606 AC: 9256 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2784 AN: 3470

East Asian (EAS) AF: 0.191 AC: 982 AN: 5136

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4820

European-Finnish (FIN) AF: 0.572 AC: 6026 AN: 10536

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47400 AN: 67926

Other (OTH) AF: 0.686 AC: 1443 AN: 2104

Alfa AF: 0.688 Hom.: 148381

Bravo AF: 0.665

Asia WGS AF: 0.357 AC: 1244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.77
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7191958; hg19: chr16-50332173;