X-153762178-A-C

Variant names:

• chrX-153762178-A-C
• rs4898439
• NR_199698.1:n.1258T>G

Variant summary

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

The NR_199698.1(PLXNB3-AS1):​n.1258T>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 NR_199698.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_199698.1. 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_199698.1		n.1258T>G		non_coding_transcript_exon	Exon 4 of 4
	PLXNB3-AS1	NR_199699.1		n.1221T>G		non_coding_transcript_exon	Exon 4 of 4
	PLXNB3-AS1	NR_199700.1		n.1253T>G		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLXNB3-AS1	ENST00000416854.1	TSL:5	n.122-1565T>G		intron	N/A
	PLXNB3-AS1	ENST00000434284.1	TSL:3	n.71+4205T>G		intron	N/A
	PLXNB3-AS1	ENST00000815145.1		n.267+1185T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 32807 AN: 110170 Hom.: 4773 Cov.: 22

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

African (AFR) AF: 0.536 AC: 16167 AN: 30153

American (AMR) AF: 0.392 AC: 4056 AN: 10337

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 526 AN: 2625

East Asian (EAS) AF: 0.513 AC: 1781 AN: 3475

South Asian (SAS) AF: 0.485 AC: 1260 AN: 2598

European-Finnish (FIN) AF: 0.151 AC: 892 AN: 5898

Middle Eastern (MID) AF: 0.256 AC: 55 AN: 215

European-Non Finnish (NFE) AF: 0.144 AC: 7608 AN: 52741

Other (OTH) AF: 0.294 AC: 444 AN: 1508

Alfa AF: 0.219 Hom.: 22416

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.78
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4898439; hg19: chrX-153027633;