rs2391996

Positions:

• chr7-31674353-G-A
• chr7-31674353-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047420441.1(PDE1C):​c.2055+36640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,050 control chromosomes in the GnomAD database, including 38,319 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 0.71 (38319 hom., cov: 33)
• Consequence: PDE1C XM_047420441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

Genes affected

PDE1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE1C	XM_047420441.1	c.2055+36640C>T		intron_variant			XP_047276397.1
PDE1C	XM_047420442.1	c.2055+36640C>T		intron_variant			XP_047276398.1
PDE1C	XM_047420443.1	c.2055+36640C>T		intron_variant			XP_047276399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107371 AN: 151932 Hom.: 38314 Cov.: 33

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.706 AC: 107409 AN: 152050 Hom.: 38319 Cov.: 33 AF XY: 0.706 AC XY: 52440 AN XY: 74302

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.706

Alfa AF: 0.728 Hom.: 14808

Bravo AF: 0.710

Asia WGS AF: 0.712 AC: 2474 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2391996; hg19: chr7-31713967;