chr1-242129492-C-T

Variant names:

• chr1-242129492-C-T
• rs1898153
• NM_001372062.1:c.736-4827G>A

Variant summary

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

The NM_001372062.1(PLD5):​c.736-4827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,014 control chromosomes in the GnomAD database, including 11,994 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 0.38 (11994 hom., cov: 33)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372062.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	NM_001372062.1	MANE Select	c.736-4827G>A		intron	N/A	NP_001358991.1
	PLD5	NM_001195811.2		c.550-4827G>A		intron	N/A	NP_001182740.1
	PLD5	NM_001320272.2		c.460-4827G>A		intron	N/A	NP_001307201.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	ENST00000536534.7	TSL:1 MANE Select	c.736-4827G>A		intron	N/A	ENSP00000440896.1
	PLD5	ENST00000427495.5	TSL:1	c.550-4827G>A		intron	N/A	ENSP00000401285.1
	PLD5	ENST00000442594.6	TSL:5	c.736-4827G>A		intron	N/A	ENSP00000414188.3

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58417 AN: 151898 Hom.: 11989 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.384 AC: 58444 AN: 152014 Hom.: 11994 Cov.: 33 AF XY: 0.388 AC XY: 28804 AN XY: 74290

African (AFR) AF: 0.258 AC: 10704 AN: 41474

American (AMR) AF: 0.472 AC: 7213 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3149 AN: 5162

South Asian (SAS) AF: 0.485 AC: 2340 AN: 4826

European-Finnish (FIN) AF: 0.435 AC: 4586 AN: 10532

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27940 AN: 67978

Other (OTH) AF: 0.398 AC: 838 AN: 2104

Alfa AF: 0.392 Hom.: 2077

Bravo AF: 0.382

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.79
PhyloP100		0.24
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: rs1898153; hg19: chr1-242292794;