16-50262083-C-G

Variant names:

• chr16-50262083-C-G
• rs4611457
• ENST00000564044.5:c.-64+15880C>G

Variant summary

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

The ENST00000564044.5(ADCY7):​c.-64+15880C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,936 control chromosomes in the GnomAD database, including 20,045 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 0.51 (20045 hom., cov: 31)
• Consequence: ADCY7 ENST00000564044.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 2 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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564044.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY7	ENST00000564044.5	TSL:3	c.-64+15880C>G		intron	N/A	ENSP00000501222.1	A0A669KBF7
	ADCY7	ENST00000564965.5	TSL:4	c.-269+15880C>G		intron	N/A	ENSP00000460636.1	I3L3Q5

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77521 AN: 151816 Hom.: 20052 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.510 AC: 77535 AN: 151936 Hom.: 20045 Cov.: 31 AF XY: 0.520 AC XY: 38593 AN XY: 74250

African (AFR) AF: 0.542 AC: 22473 AN: 41428

American (AMR) AF: 0.475 AC: 7242 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1729 AN: 3464

East Asian (EAS) AF: 0.676 AC: 3481 AN: 5148

South Asian (SAS) AF: 0.659 AC: 3175 AN: 4820

European-Finnish (FIN) AF: 0.594 AC: 6277 AN: 10562

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31629 AN: 67952

Other (OTH) AF: 0.515 AC: 1083 AN: 2104

Alfa AF: 0.330 Hom.: 777

Bravo AF: 0.500

Asia WGS AF: 0.658 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		0.043

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4611457; hg19: chr16-50295994;