10-19918420-C-T

Position:

• chr10-19918420-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.113-83355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,980 control chromosomes in the GnomAD database, including 18,036 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 0.46 (18036 hom., cov: 32)
• Consequence: PLXDC2 NM_032812.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLXDC2	NM_032812.9	c.113-83355C>T		intron_variant		ENST00000377252.5	NP_116201.7
PLXDC2	NM_001282736.2	c.113-83355C>T		intron_variant			NP_001269665.1
PLXDC2	XM_011519750.3	c.113-83355C>T		intron_variant			XP_011518052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLXDC2	ENST00000377252.5	c.113-83355C>T		intron_variant		1	NM_032812.9	ENSP00000366460	P1
PLXDC2	ENST00000377242.7	c.113-83355C>T		intron_variant		1		ENSP00000366450

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70365 AN: 151860 Hom.: 18030 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.463 AC: 70390 AN: 151980 Hom.: 18036 Cov.: 32 AF XY: 0.463 AC XY: 34369 AN XY: 74272

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.495

Alfa AF: 0.556 Hom.: 48413

Bravo AF: 0.447

Asia WGS AF: 0.595 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.31
DANN	Benign	0.51

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: rs2038912; hg19: chr10-20207349;