rs1367951

Positions:

• chr1-213952170-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+13901T>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 0.389 in 151,972 control chromosomes in the GnomAD database, including 11,859 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 (11859 hom., cov: 32)
• Consequence: PROX1-AS1 NR_037850.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PROX1-AS1	NR_037850.2	n.299+13901T>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+13901T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59135 AN: 151854 Hom.: 11854 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.389 AC: 59158 AN: 151972 Hom.: 11859 Cov.: 32 AF XY: 0.392 AC XY: 29119 AN XY: 74278

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.432

Alfa AF: 0.409 Hom.: 3198

Bravo AF: 0.382

Asia WGS AF: 0.258 AC: 900 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	8.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1367951; hg19: chr1-214125513;