1-242443086-T-C

Variant names:

• chr1-242443086-T-C
• rs2810034
• NM_001372062.1:c.189+81002A>G

Variant summary

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

The ENST00000536534.7(PLD5):​c.189+81002A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,040 control chromosomes in the GnomAD database, including 9,827 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 0.36 (9827 hom., cov: 32)
• Consequence: PLD5 ENST00000536534.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536534.7. 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.189+81002A>G		intron	N/A	NP_001358991.1
	PLD5	NM_001195811.2		c.3+6268A>G		intron	N/A	NP_001182740.1
	PLD5	NM_001320272.2		c.-95+81002A>G		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.189+81002A>G		intron	N/A	ENSP00000440896.1
	PLD5	ENST00000427495.5	TSL:1	c.3+6268A>G		intron	N/A	ENSP00000401285.1
	PLD5	ENST00000442594.6	TSL:5	c.189+81002A>G		intron	N/A	ENSP00000414188.3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53969 AN: 151922 Hom.: 9814 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.355 AC: 54031 AN: 152040 Hom.: 9827 Cov.: 32 AF XY: 0.353 AC XY: 26220 AN XY: 74286

African (AFR) AF: 0.366 AC: 15194 AN: 41460

American (AMR) AF: 0.438 AC: 6681 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3470

East Asian (EAS) AF: 0.174 AC: 901 AN: 5176

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4818

European-Finnish (FIN) AF: 0.316 AC: 3326 AN: 10528

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24229 AN: 68006

Other (OTH) AF: 0.375 AC: 793 AN: 2114

Alfa AF: 0.354 Hom.: 36764

Bravo AF: 0.367

Asia WGS AF: 0.253 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.60
PhyloP100		-1.4
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: rs2810034; hg19: chr1-242606388;