rs12097667

Positions:

• chr1-242384646-C-A
• chr1-242384646-C-T

Variant summary

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

The NM_001372062.1(PLD5):​c.190-36404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,144 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD5	NM_001372062.1	c.190-36404G>T		intron_variant		ENST00000536534.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD5	ENST00000536534.7	c.190-36404G>T		intron_variant		1	NM_001372062.1	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25871 AN: 152026 Hom.: 2410 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.170 AC: 25910 AN: 152144 Hom.: 2409 Cov.: 32 AF XY: 0.172 AC XY: 12797 AN XY: 74384

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0736

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.167

Alfa AF: 0.137 Hom.: 2166

Bravo AF: 0.182

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.97
DANN	Benign	0.37

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: rs12097667; hg19: chr1-242547948;