chr1-213944747-C-A

Variant names:

• chr1-213944747-C-A
• rs340849
• ENST00000413560.5:n.188+21324G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413560.5(PROX1-AS1):​n.188+21324G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,946 control chromosomes in the GnomAD database, including 12,913 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 0.39 (12913 hom., cov: 31)
• Consequence: PROX1-AS1 ENST00000413560.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 6 publications found

Genes affected

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

ENSG00000225233 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413560.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROX1-AS1	NR_037850.2		n.299+21324G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROX1-AS1	ENST00000413560.5	TSL:5	n.188+21324G>T		intron	N/A
	PROX1-AS1	ENST00000433082.6	TSL:5	n.276+21324G>T		intron	N/A
	PROX1-AS1	ENST00000593620.5	TSL:5	n.217+10276G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58761 AN: 151826 Hom.: 12913 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.387 AC: 58766 AN: 151946 Hom.: 12913 Cov.: 31 AF XY: 0.382 AC XY: 28362 AN XY: 74260

African (AFR) AF: 0.176 AC: 7297 AN: 41466

American (AMR) AF: 0.358 AC: 5465 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1471 AN: 3460

East Asian (EAS) AF: 0.471 AC: 2426 AN: 5150

South Asian (SAS) AF: 0.501 AC: 2413 AN: 4818

European-Finnish (FIN) AF: 0.397 AC: 4190 AN: 10564

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.501 AC: 34030 AN: 67926

Other (OTH) AF: 0.387 AC: 816 AN: 2108

Alfa AF: 0.451 Hom.: 29438

Bravo AF: 0.370

Asia WGS AF: 0.451 AC: 1567 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.79
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs340849; hg19: chr1-214118090;