1-242155169-A-G

Variant names:

• chr1-242155169-A-G
• rs2217881
• NM_001372062.1:c.736-30504T>C

Variant summary

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

The NM_001372062.1(PLD5):​c.736-30504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,152 control chromosomes in the GnomAD database, including 54,457 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 0.84 (54457 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• 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]

ENSG00000272865 (HGNC:41171):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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.736-30504T>C		intron	N/A	NP_001358991.1
	PLD5	NM_001195811.2		c.550-30504T>C		intron	N/A	NP_001182740.1
	PLD5	NM_001320272.2		c.460-30504T>C		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.736-30504T>C		intron	N/A	ENSP00000440896.1
	PLD5	ENST00000427495.5	TSL:1	c.550-30504T>C		intron	N/A	ENSP00000401285.1
	PLD5	ENST00000442594.6	TSL:5	c.736-30504T>C		intron	N/A	ENSP00000414188.3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128034 AN: 152034 Hom.: 54402 Cov.: 32

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.842 AC: 128148 AN: 152152 Hom.: 54457 Cov.: 32 AF XY: 0.846 AC XY: 62948 AN XY: 74396

African (AFR) AF: 0.955 AC: 39638 AN: 41514

American (AMR) AF: 0.837 AC: 12800 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2844 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4780 AN: 5182

South Asian (SAS) AF: 0.943 AC: 4543 AN: 4820

European-Finnish (FIN) AF: 0.793 AC: 8378 AN: 10570

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52439 AN: 67990

Other (OTH) AF: 0.836 AC: 1766 AN: 2112

Alfa AF: 0.789 Hom.: 20206

Bravo AF: 0.849

Asia WGS AF: 0.917 AC: 3189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		-0.86
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: rs2217881; hg19: chr1-242318471;