rs2302679

Variant names:

• chr16-50311867-T-A
• rs2302679
• NM_001114.5:c.2448+81T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-50311867-T-A
• chr16-50311867-T-C
• chr16-50311867-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001114.5(ADCY7):​c.2448+81T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0000075 (0 hom., cov: 20)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADCY7 NM_001114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 6 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY7	NM_001114.5	c.2448+81T>A		intron_variant	Intron 20 of 25	ENST00000673801.1	NP_001105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY7	ENST00000673801.1	c.2448+81T>A		intron_variant	Intron 20 of 25		NM_001114.5	ENSP00000501053.1
ADCY7	ENST00000254235.7	c.2448+81T>A		intron_variant	Intron 19 of 24	1		ENSP00000254235.3
ADCY7	ENST00000394697.7	c.2448+81T>A		intron_variant	Intron 20 of 25	5		ENSP00000378187.2
ADCY7	ENST00000673973.1	n.*820+81T>A		intron_variant	Intron 20 of 25			ENSP00000501223.1

Frequencies

GnomAD3 genomes AF: 0.00000754 AC: 1 AN: 132590 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000740

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1150946 Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0 AN XY: 583010

African (AFR) AF: 0.00 AC: 0 AN: 26852

American (AMR) AF: 0.00 AC: 0 AN: 43108

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23008

East Asian (EAS) AF: 0.00 AC: 0 AN: 29698

South Asian (SAS) AF: 0.00 AC: 0 AN: 77548

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45564

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4026

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 852372

Other (OTH) AF: 0.00 AC: 0 AN: 48770

GnomAD4 genome AF: 0.00000754 AC: 1 AN: 132590 Hom.: 0 Cov.: 20 AF XY: 0.0000157 AC XY: 1 AN XY: 63606

African (AFR) AF: 0.00 AC: 0 AN: 35076

American (AMR) AF: 0.0000740 AC: 1 AN: 13514

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3304

East Asian (EAS) AF: 0.00 AC: 0 AN: 3574

South Asian (SAS) AF: 0.00 AC: 0 AN: 4164

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6900

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 256

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 63108

Other (OTH) AF: 0.00 AC: 0 AN: 1834

Alfa AF: 0.00 Hom.: 35501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.041
DANN	Benign	0.57
PhyloP100		-0.26

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: rs2302679; hg19: chr16-50345778;