rs1571942

Positions:

• chr10-20253705-A-G

Variant summary

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

The NM_032812.9(PLXDC2):​c.1473+8200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,160 control chromosomes in the GnomAD database, including 1,683 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 0.15 (1683 hom., cov: 32)
• Consequence: PLXDC2 NM_032812.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

Genes affected

PLXDC2 (HGNC:21013): (plexin domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXDC2	NM_032812.9	c.1473+8200A>G		intron_variant		ENST00000377252.5
PLXDC2	NM_001282736.2	c.1326+8200A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXDC2	ENST00000377252.5	c.1473+8200A>G		intron_variant		1	NM_032812.9	P1
PLXDC2	ENST00000377242.7	c.1326+8200A>G		intron_variant		1
PLXDC2	ENST00000377238.2	n.1248+8200A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22385 AN: 152042 Hom.: 1680 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22396 AN: 152160 Hom.: 1683 Cov.: 32 AF XY: 0.146 AC XY: 10863 AN XY: 74398

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0931

Gnomad4 SAS AF: 0.0482

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.137

Alfa AF: 0.144 Hom.: 2684

Bravo AF: 0.147

Asia WGS AF: 0.0800 AC: 279 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571942; hg19: chr10-20542634;