1-46135245-A-G

Position:

• chr1-46135245-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+40983T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,988 control chromosomes in the GnomAD database, including 32,142 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 0.65 (32142 hom., cov: 31)
• Consequence: P3R3URF-PIK3R3 NM_001303427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.69

Genes affected

P3R3URF-PIK3R3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P3R3URF-PIK3R3	NM_001303427.2	c.244+40983T>C		intron_variant			NP_001290356.1
LOC101929626	NR_125987.1	n.144+591A>G		intron_variant, non_coding_transcript_variant
PIK3R3	NM_001328648.1	c.-27+39592T>C		intron_variant			NP_001315577.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000452785.2	n.124+591A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98652 AN: 151870 Hom.: 32127 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.649 AC: 98699 AN: 151988 Hom.: 32142 Cov.: 31 AF XY: 0.649 AC XY: 48206 AN XY: 74274

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.645

Alfa AF: 0.668 Hom.: 36772

Bravo AF: 0.651

Asia WGS AF: 0.637 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	18
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1707302; hg19: chr1-46600917; COSMIC: COSV53106145; COSMIC: COSV53106145;