1-242368352-T-C

Variant names:

• chr1-242368352-T-C
• rs1439523
• NM_001372062.1:c.190-20110A>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.190-20110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,138 control chromosomes in the GnomAD database, including 62,112 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 0.90 (62112 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLD5	NM_001372062.1	c.190-20110A>G		intron_variant	Intron 1 of 9	ENST00000536534.7	NP_001358991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLD5	ENST00000536534.7	c.190-20110A>G		intron_variant	Intron 1 of 9	1	NM_001372062.1	ENSP00000440896.1

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136169 AN: 152020 Hom.: 62112 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.895 AC: 136204 AN: 152138 Hom.: 62112 Cov.: 32 AF XY: 0.897 AC XY: 66713 AN XY: 74368

African (AFR) AF: 0.704 AC: 29190 AN: 41448

American (AMR) AF: 0.932 AC: 14244 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3196 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4700 AN: 5162

South Asian (SAS) AF: 0.942 AC: 4548 AN: 4826

European-Finnish (FIN) AF: 0.995 AC: 10543 AN: 10594

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66686 AN: 68036

Other (OTH) AF: 0.911 AC: 1924 AN: 2112

Alfa AF: 0.942 Hom.: 177629

Bravo AF: 0.881

Asia WGS AF: 0.873 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		-0.93
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: rs1439523; hg19: chr1-242531654;