1-242111606-G-T

Variant names:

• chr1-242111606-G-T
• rs10803016
• NM_001372062.1:c.1070+2284C>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.1070+2284C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,752 control chromosomes in the GnomAD database, including 18,402 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 0.49 (18402 hom., cov: 31)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 6 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 = 0.578 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	NM_001372062.1	MANE Select	c.1070+2284C>A		intron	N/A	NP_001358991.1	Q8N7P1-1
	PLD5	NM_001195811.2		c.884+2284C>A		intron	N/A	NP_001182740.1	Q8N7P1-4
	PLD5	NM_001320272.2		c.794+2284C>A		intron	N/A	NP_001307201.1	Q8N7P1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	ENST00000536534.7	TSL:1 MANE Select	c.1070+2284C>A		intron	N/A	ENSP00000440896.1	Q8N7P1-1
	PLD5	ENST00000427495.5	TSL:1	c.884+2284C>A		intron	N/A	ENSP00000401285.1	Q8N7P1-4
	PLD5	ENST00000442594.6	TSL:5	c.1070+2284C>A		intron	N/A	ENSP00000414188.3	Q8N7P1-1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74293 AN: 151632 Hom.: 18390 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.490 AC: 74356 AN: 151752 Hom.: 18402 Cov.: 31 AF XY: 0.491 AC XY: 36417 AN XY: 74110

African (AFR) AF: 0.530 AC: 21920 AN: 41360

American (AMR) AF: 0.528 AC: 8046 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3075 AN: 5162

South Asian (SAS) AF: 0.488 AC: 2347 AN: 4806

European-Finnish (FIN) AF: 0.501 AC: 5253 AN: 10478

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.455 AC: 30908 AN: 67930

Other (OTH) AF: 0.486 AC: 1023 AN: 2104

Alfa AF: 0.457 Hom.: 21131

Bravo AF: 0.497

Asia WGS AF: 0.529 AC: 1837 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.67
PhyloP100		0.37
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: rs10803016; hg19: chr1-242274908;