rs723632

chr1-213886409-G-Cchr1-213886409-G-T

Variant summary

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

The NR_037850.2(PROX1-AS1):n.505+8254C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,122 control chromosomes in the GnomAD database, including 44,931 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 (44931 hom., cov: 32)
• Consequence: PROX1-AS1 NR_037850.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

Genes affected

PROX1-AS1 (HGNC:43656): (PROX1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROX1-AS1	NR_037850.2	n.505+8254C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PROX1-AS1	ENST00000433082.6	n.482+8254C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107499 AN: 152004 Hom.: 44940 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.707 AC: 107498 AN: 152122 Hom.: 44931 Cov.: 32 AF XY: 0.707 AC XY: 52563 AN XY: 74360

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.784

Alfa AF: 0.722 Hom.: 3091

Bravo AF: 0.679

Asia WGS AF: 0.711 AC: 2472 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723632; hg19: chr1-214059752;