rs10508605

chr10-19965072-C-Gchr10-19965072-C-T

Variant summary

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

The NM_032812.9(PLXDC2):c.113-36703C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0522 in 152,234 control chromosomes in the GnomAD database, including 268 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 0.052 (268 hom., cov: 32)
• Consequence: PLXDC2 NM_032812.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXDC2	NM_032812.9	c.113-36703C>G		intron_variant		ENST00000377252.5
PLXDC2	NM_001282736.2	c.113-36703C>G		intron_variant
PLXDC2	XM_011519750.3	c.113-36703C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXDC2	ENST00000377252.5	c.113-36703C>G		intron_variant		1	NM_032812.9	P1
PLXDC2	ENST00000377242.7	c.113-36703C>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7950 AN: 152116 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0522 AC: 7945 AN: 152234 Hom.: 268 Cov.: 32 AF XY: 0.0496 AC XY: 3694 AN XY: 74436

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0676

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0764

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0243 Hom.: 12

Bravo AF: 0.0520

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.2
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: rs10508605; hg19: chr10-20254001;