1-213952511-A-G

Position:

• chr1-213952511-A-G

Variant summary

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

The NR_037850.2(PROX1-AS1):​n.299+13560T>C 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 0.503 in 151,798 control chromosomes in the GnomAD database, including 20,435 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 0.50 (20435 hom., cov: 31)
• Consequence: PROX1-AS1 NR_037850.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) 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
PROX1-AS1	NR_037850.2	n.299+13560T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PROX1-AS1	ENST00000433082.6	n.276+13560T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76293 AN: 151680 Hom.: 20400 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.503 AC: 76385 AN: 151798 Hom.: 20435 Cov.: 31 AF XY: 0.508 AC XY: 37696 AN XY: 74174

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.503

Alfa AF: 0.382 Hom.: 1740

Bravo AF: 0.515

Asia WGS AF: 0.499 AC: 1735 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2075425; hg19: chr1-214125854;