chr10-38249843-A-G

Position:

• chr10-38249843-A-G

Variant summary

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

The ENST00000640275.1(PLD5P1):​n.*789+1778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,060 control chromosomes in the GnomAD database, including 15,572 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 0.45 (15572 hom., cov: 32)
• Consequence: PLD5P1 ENST00000640275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

PLD5P1 (HGNC:55072): (PLD5 pseudogene 1) Predicted to be involved in regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38249843A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLD5P1	ENST00000640275.1	n.*789+1778A>G		intron_variant		5		ENSP00000491560.1
ENSG00000226113	ENST00000450980.1	n.144+1778A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68568 AN: 150944 Hom.: 15535 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.455 AC: 68658 AN: 151060 Hom.: 15572 Cov.: 32 AF XY: 0.449 AC XY: 33169 AN XY: 73830

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.481

Alfa AF: 0.450 Hom.: 1693

Asia WGS AF: 0.486 AC: 1691 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1740752; hg19: chr10-38538771;