rs943124

Positions:

• chr10-19863804-T-A

Variant summary

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

The NM_032812.9(PLXDC2):​c.112+46613T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 140,064 control chromosomes in the GnomAD database, including 11,276 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 0.41 (11276 hom., cov: 32)
• Consequence: PLXDC2 NM_032812.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLXDC2	NM_032812.9	c.112+46613T>A		intron_variant		ENST00000377252.5	NP_116201.7
PLXDC2	NM_001282736.2	c.112+46613T>A		intron_variant			NP_001269665.1
PLXDC2	XM_011519750.3	c.112+46613T>A		intron_variant			XP_011518052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLXDC2	ENST00000377252.5	c.112+46613T>A		intron_variant		1	NM_032812.9	ENSP00000366460.3
PLXDC2	ENST00000377242.7	c.112+46613T>A		intron_variant		1		ENSP00000366450.3

Frequencies

GnomAD3 genomes AF: 0.408 AC: 57094 AN: 139950 Hom.: 11264 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.408 AC: 57138 AN: 140064 Hom.: 11276 Cov.: 32 AF XY: 0.411 AC XY: 27885 AN XY: 67812

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.428

Alfa AF: 0.352 Hom.: 1198

Bravo AF: 0.387

Asia WGS AF: 0.213 AC: 739 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.71

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: rs943124; hg19: chr10-20152733;