16-50262083-C-G

Position:

• chr16-50262083-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY7	XM_011522837.4	c.-269+15880C>G		intron_variant			XP_011521139.1
ADCY7	XM_047433551.1	c.-269+17144C>G		intron_variant			XP_047289507.1
ADCY7	XM_047433552.1	c.-299+15880C>G		intron_variant			XP_047289508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCY7	ENST00000564044.5	c.-64+15880C>G		intron_variant		3		ENSP00000501222.1
ADCY7	ENST00000564965.5	c.-269+15880C>G		intron_variant		4		ENSP00000460636.1

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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.515

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4611457; hg19: chr16-50295994;