rs10508606

Positions:

• chr10-19987202-T-G

Variant summary

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

The NM_032812.9(PLXDC2):​c.113-14573T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,308 control chromosomes in the GnomAD database, including 275 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 0.053 (275 hom., cov: 32)
• Consequence: PLXDC2 NM_032812.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLXDC2	NM_032812.9	c.113-14573T>G		intron_variant		ENST00000377252.5	NP_116201.7
PLXDC2	NM_001282736.2	c.113-14573T>G		intron_variant			NP_001269665.1
PLXDC2	XM_011519750.3	c.113-14573T>G		intron_variant			XP_011518052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLXDC2	ENST00000377252.5	c.113-14573T>G		intron_variant		1	NM_032812.9	ENSP00000366460.3
PLXDC2	ENST00000377242.7	c.113-14573T>G		intron_variant		1		ENSP00000366450.3

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8031 AN: 152190 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0527 AC: 8026 AN: 152308 Hom.: 275 Cov.: 32 AF XY: 0.0501 AC XY: 3735 AN XY: 74484

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.0127

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0769

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0646 Hom.: 176

Bravo AF: 0.0527

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.67

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: rs10508606; hg19: chr10-20276131;