rs1740752

Variant names:

• chr10-38249843-A-G
• rs1740752
• ENST00000640275.1:n.*789+1778A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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]

ENSG00000226113 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5P1	ENST00000640275.1	TSL:5	n.*789+1778A>G		intron	N/A	ENSP00000491560.1
	ENSG00000226113	ENST00000450980.1	TSL:6	n.144+1778A>G		intron	N/A

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

African (AFR) AF: 0.487 AC: 20025 AN: 41112

American (AMR) AF: 0.498 AC: 7543 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3464

East Asian (EAS) AF: 0.548 AC: 2787 AN: 5084

South Asian (SAS) AF: 0.335 AC: 1605 AN: 4784

European-Finnish (FIN) AF: 0.334 AC: 3511 AN: 10500

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.445 AC: 30132 AN: 67668

Other (OTH) AF: 0.481 AC: 1012 AN: 2102

Alfa AF: 0.450 Hom.: 1693

Asia WGS AF: 0.486 AC: 1691 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
DANN	Benign	0.63
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1740752; hg19: chr10-38538771;