X-153750499-C-T

Variant names:

• chrX-153750499-C-T
• rs4898437
• ENST00000434284.1:n.72-11921G>A

Variant summary

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

The ENST00000434284.1(PLXNB3-AS1):​n.72-11921G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 110,140 control chromosomes in the GnomAD database, including 5,768 homozygotes. There are 10,114 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 0.31 (5768 hom., 10114 hem., cov: 22)
• Consequence: PLXNB3-AS1 ENST00000434284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 2 publications found

Genes affected

PLXNB3-AS1 (HGNC:40454): (PLXNB3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434284.1. 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
	PLXNB3-AS1	NR_199693.1		n.90-11921G>A		intron	N/A
	PLXNB3-AS1	NR_199694.1		n.198-11921G>A		intron	N/A
	PLXNB3-AS1	NR_199695.1		n.309-11921G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLXNB3-AS1	ENST00000434284.1	TSL:3	n.72-11921G>A		intron	N/A
	PLXNB3-AS1	ENST00000815145.1		n.268-2849G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 34359 AN: 110084 Hom.: 5764 Cov.: 22

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.312 AC: 34416 AN: 110140 Hom.: 5768 Cov.: 22 AF XY: 0.312 AC XY: 10114 AN XY: 32446

African (AFR) AF: 0.619 AC: 18633 AN: 30113

American (AMR) AF: 0.389 AC: 4000 AN: 10270

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 498 AN: 2638

East Asian (EAS) AF: 0.544 AC: 1883 AN: 3463

South Asian (SAS) AF: 0.479 AC: 1223 AN: 2554

European-Finnish (FIN) AF: 0.145 AC: 850 AN: 5843

Middle Eastern (MID) AF: 0.235 AC: 51 AN: 217

European-Non Finnish (NFE) AF: 0.128 AC: 6753 AN: 52879

Other (OTH) AF: 0.308 AC: 457 AN: 1483

Alfa AF: 0.242 Hom.: 19167

Bravo AF: 0.348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.71
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4898437; hg19: chrX-153015953;