10-19965072-C-G

Variant names:

• chr10-19965072-C-G
• rs10508605
• NM_032812.9:c.113-36703C>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.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
• Publications: 0 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=-0.8).
• 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 rank	MANE	Protein	UniProt
PLXDC2	NM_032812.9	c.113-36703C>G		intron_variant	Intron 1 of 13	ENST00000377252.5	NP_116201.7
PLXDC2	NM_001282736.2	c.113-36703C>G		intron_variant	Intron 1 of 12		NP_001269665.1
PLXDC2	XM_011519750.3	c.113-36703C>G		intron_variant	Intron 1 of 13		XP_011518052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLXDC2	ENST00000377252.5	c.113-36703C>G		intron_variant	Intron 1 of 13	1	NM_032812.9	ENSP00000366460.3
PLXDC2	ENST00000377242.7	c.113-36703C>G		intron_variant	Intron 1 of 12	1		ENSP00000366450.3

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

African (AFR) AF: 0.0157 AC: 651 AN: 41538

American (AMR) AF: 0.0676 AC: 1034 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5174

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4826

European-Finnish (FIN) AF: 0.0403 AC: 427 AN: 10606

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0764 AC: 5198 AN: 68008

Other (OTH) AF: 0.0573 AC: 121 AN: 2110

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
PhyloP100		-0.12
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: rs10508605; hg19: chr10-20254001;