1-242192726-T-C

Variant names:

• chr1-242192726-T-C
• rs316823
• NM_001372062.1:c.735+27262A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001372062.1(PLD5):​c.735+27262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,102 control chromosomes in the GnomAD database, including 54,771 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 0.85 (54771 hom., cov: 31)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 3 publications found

Genes affected

PLD5 (HGNC:26879): (phospholipase D family member 5) Predicted to enable catalytic activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000272865 (HGNC:41171):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLD5	NM_001372062.1	c.735+27262A>G		intron_variant	Intron 5 of 9	ENST00000536534.7	NP_001358991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLD5	ENST00000536534.7	c.735+27262A>G		intron_variant	Intron 5 of 9	1	NM_001372062.1	ENSP00000440896.1

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128430 AN: 151984 Hom.: 54712 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.845 AC: 128548 AN: 152102 Hom.: 54771 Cov.: 31 AF XY: 0.850 AC XY: 63198 AN XY: 74344

African (AFR) AF: 0.950 AC: 39414 AN: 41478

American (AMR) AF: 0.841 AC: 12856 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2862 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4780 AN: 5158

South Asian (SAS) AF: 0.944 AC: 4551 AN: 4820

European-Finnish (FIN) AF: 0.824 AC: 8727 AN: 10592

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52635 AN: 67988

Other (OTH) AF: 0.836 AC: 1763 AN: 2108

Alfa AF: 0.821 Hom.: 8313

Bravo AF: 0.850

Asia WGS AF: 0.920 AC: 3200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		0.012
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: rs316823; hg19: chr1-242356028;