10-20253705-A-G

Variant names:

• chr10-20253705-A-G
• rs1571942
• NM_032812.9:c.1473+8200A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLXDC2	NM_032812.9	c.1473+8200A>G		intron_variant	Intron 13 of 13	ENST00000377252.5	NP_116201.7
PLXDC2	NM_001282736.2	c.1326+8200A>G		intron_variant	Intron 12 of 12		NP_001269665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLXDC2	ENST00000377252.5	c.1473+8200A>G		intron_variant	Intron 13 of 13	1	NM_032812.9	ENSP00000366460.3
PLXDC2	ENST00000377242.7	c.1326+8200A>G		intron_variant	Intron 12 of 12	1		ENSP00000366450.3
PLXDC2	ENST00000377238.2	n.1248+8200A>G		intron_variant	Intron 12 of 12	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

African (AFR) AF: 0.150 AC: 6244 AN: 41512

American (AMR) AF: 0.149 AC: 2280 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.0931 AC: 482 AN: 5178

South Asian (SAS) AF: 0.0482 AC: 233 AN: 4830

European-Finnish (FIN) AF: 0.169 AC: 1792 AN: 10580

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10444 AN: 68000

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.147 Hom.: 6129

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
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1571942; hg19: chr10-20542634;