rs4898439

Positions:

• chrX-153762178-A-C
• chrX-153762178-A-T

Variant summary

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

The XR_430559.4(PLXNB3-AS1):​n.1237T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 110,225 control chromosomes in the GnomAD database, including 4,776 homozygotes. There are 9,705 hemizygotes in GnomAD. 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 0.30 (4776 hom., 9705 hem., cov: 22)
• Consequence: PLXNB3-AS1 XR_430559.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

PLXNB3-AS1 (HGNC:):

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 = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLXNB3-AS1	XR_007068351.1	n.1242T>G		non_coding_transcript_exon_variant	4/4
PLXNB3-AS1	XR_007068354.1	n.1247T>G		non_coding_transcript_exon_variant	4/4
PLXNB3-AS1	XR_430559.4	n.1237T>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLXNB3-AS1	ENST00000416854.1	n.122-1565T>G		intron_variant		5
PLXNB3-AS1	ENST00000434284.1	n.71+4205T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.298 AC: 32807 AN: 110170 Hom.: 4773 Cov.: 22 AF XY: 0.297 AC XY: 9660 AN XY: 32476

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.298 AC: 32858 AN: 110225 Hom.: 4776 Cov.: 22 AF XY: 0.298 AC XY: 9705 AN XY: 32541

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.294

Alfa AF: 0.185 Hom.: 12971

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
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: rs4898439; hg19: chrX-153027633;