rs1473840

Positions:

• chr1-46135525-A-G

Variant summary

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

The NM_001303427.2(P3R3URF-PIK3R3):​c.244+40703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,018 control chromosomes in the GnomAD database, including 35,636 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 0.68 (35636 hom., cov: 31)
• Consequence: P3R3URF-PIK3R3 NM_001303427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

Genes affected

P3R3URF-PIK3R3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P3R3URF-PIK3R3	NM_001303427.2	c.244+40703T>C		intron_variant			NP_001290356.1
LOC101929626	NR_125987.1	n.144+871A>G		intron_variant, non_coding_transcript_variant
PIK3R3	NM_001328648.1	c.-27+39312T>C		intron_variant			NP_001315577.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000452785.2	n.124+871A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103824 AN: 151900 Hom.: 35618 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.683 AC: 103874 AN: 152018 Hom.: 35636 Cov.: 31 AF XY: 0.681 AC XY: 50619 AN XY: 74296

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.662

Alfa AF: 0.668 Hom.: 4394

Bravo AF: 0.690

Asia WGS AF: 0.642 AC: 2230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1473840; hg19: chr1-46601197; COSMIC: COSV53106151; COSMIC: COSV53106151;