rs2196826

Positions:

• chr1-242383031-G-A
• chr1-242383031-G-C

Variant summary

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

The NM_001372062.1(PLD5):​c.190-34789C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,996 control chromosomes in the GnomAD database, including 5,760 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 0.27 (5760 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLD5	NM_001372062.1	c.190-34789C>T		intron_variant		ENST00000536534.7	NP_001358991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLD5	ENST00000536534.7	c.190-34789C>T		intron_variant		1	NM_001372062.1	ENSP00000440896	P1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40330 AN: 151878 Hom.: 5765 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.00773

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.265 AC: 40329 AN: 151996 Hom.: 5760 Cov.: 32 AF XY: 0.264 AC XY: 19606 AN XY: 74290

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.00756

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.311

Alfa AF: 0.301 Hom.: 4845

Bravo AF: 0.266

Asia WGS AF: 0.174 AC: 603 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	14
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs2196826; hg19: chr1-242546333;