chr3-171602816-T-C

Position:

• chr3-171602816-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002662.5(PLD1):​c.*262A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 426,176 control chromosomes in the GnomAD database, including 374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.040 (290 hom., cov: 32)
  • Exomes 𝑓: 0.012 (84 hom.)
• Consequence: PLD1 NM_002662.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51

Genes affected

PLD1 (HGNC:9067): (phospholipase D1) This gene encodes a phosphatidylcholine-specific phospholipase which catalyzes the hydrolysis of phosphatidylcholine in order to yield phosphatidic acid and choline. The enzyme may play a role in signal transduction and subcellular trafficking. Alternative splicing results in multiple transcript variants with both catalytic and regulatory properties. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 3-171602816-T-C is Benign according to our data. Variant chr3-171602816-T-C is described in ClinVar as [Benign]. Clinvar id is 1268822.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD1	NM_002662.5	c.*262A>G		3_prime_UTR_variant	27/27	ENST00000351298.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD1	ENST00000351298.9	c.*262A>G		3_prime_UTR_variant	27/27	1	NM_002662.5	A1
PLD1	ENST00000356327.9	c.*262A>G		3_prime_UTR_variant	26/26	1		P4

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6128 AN: 152170 Hom.: 289 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0282

GnomAD4 exome AF: 0.0124 AC: 3402 AN: 273888 Hom.: 84 Cov.: 0 AF XY: 0.0115 AC XY: 1615 AN XY: 141036

Gnomad4 AFR exome AF: 0.115

Gnomad4 AMR exome AF: 0.0153

Gnomad4 ASJ exome AF: 0.00302

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00142

Gnomad4 FIN exome AF: 0.00328

Gnomad4 NFE exome AF: 0.0106

Gnomad4 OTH exome AF: 0.0173

GnomAD4 genome AF: 0.0403 AC: 6137 AN: 152288 Hom.: 290 Cov.: 32 AF XY: 0.0384 AC XY: 2861 AN XY: 74478

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.0113

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0219 Hom.: 18

Bravo AF: 0.0450

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.45

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: rs73038024; hg19: chr3-171320606;