1-242383031-G-A

Variant names:

• chr1-242383031-G-A
• rs2196826
• NM_001372062.1:c.190-34789C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 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.190-34789C>T		intron	N/A	NP_001358991.1
	PLD5	NM_001195811.2		c.4-34789C>T		intron	N/A	NP_001182740.1
	PLD5	NM_001320272.2		c.-94-34789C>T		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.190-34789C>T		intron	N/A	ENSP00000440896.1
	PLD5	ENST00000427495.5	TSL:1	c.4-34789C>T		intron	N/A	ENSP00000401285.1
	PLD5	ENST00000442594.6	TSL:5	c.190-34789C>T		intron	N/A	ENSP00000414188.3

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

African (AFR) AF: 0.184 AC: 7637 AN: 41470

American (AMR) AF: 0.341 AC: 5200 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3472

East Asian (EAS) AF: 0.00756 AC: 39 AN: 5160

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10564

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

European-Non Finnish (NFE) AF: 0.311 AC: 21165 AN: 67950

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.301 Hom.: 7124

Bravo AF: 0.266

Asia WGS AF: 0.174 AC: 603 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	14
DANN	Benign	0.61
PhyloP100		1.1
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: rs2196826; hg19: chr1-242546333;