chr4-119564515-G-T

Variant names:

• chr4-119564515-G-T
• rs2127823
• NM_001083.4:c.993+806C>A

Variant summary

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

The NM_001083.4(PDE5A):​c.993+806C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,852 control chromosomes in the GnomAD database, including 6,558 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 0.29 (6558 hom., cov: 32)
• Consequence: PDE5A NM_001083.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 8 publications found

Genes affected

PDE5A (HGNC:8784): (phosphodiesterase 5A) This gene encodes a cGMP-binding, cGMP-specific phosphodiesterase, a member of the cyclic nucleotide phosphodiesterase family. This phosphodiesterase specifically hydrolyzes cGMP to 5'-GMP. It is involved in the regulation of intracellular concentrations of cyclic nucleotides and is important for smooth muscle relaxation in the cardiovascular system. Alternative splicing of this gene results in three transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083.4. 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
	PDE5A	NM_001083.4	MANE Select	c.993+806C>A		intron	N/A	NP_001074.2	O76074-1
	PDE5A	NM_033430.3		c.867+806C>A		intron	N/A	NP_236914.2	O76074-2
	PDE5A	NM_033437.4		c.837+806C>A		intron	N/A	NP_246273.2	G5E9C5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE5A	ENST00000354960.8	TSL:1 MANE Select	c.993+806C>A		intron	N/A	ENSP00000347046.3	O76074-1
	PDE5A	ENST00000264805.9	TSL:1	c.867+806C>A		intron	N/A	ENSP00000264805.5	O76074-2
	PDE5A	ENST00000925607.1		c.993+806C>A		intron	N/A	ENSP00000595666.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44459 AN: 151734 Hom.: 6555 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.293 AC: 44500 AN: 151852 Hom.: 6558 Cov.: 32 AF XY: 0.291 AC XY: 21586 AN XY: 74220

African (AFR) AF: 0.314 AC: 13026 AN: 41424

American (AMR) AF: 0.276 AC: 4210 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1965 AN: 5166

South Asian (SAS) AF: 0.177 AC: 851 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2745 AN: 10562

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19970 AN: 67872

Other (OTH) AF: 0.298 AC: 628 AN: 2106

Alfa AF: 0.285 Hom.: 1030

Bravo AF: 0.302

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.30
PhyloP100		0.33
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: rs2127823; hg19: chr4-120485670;