rs316838

Variant names:

• chr1-242157358-G-A
• rs316838
• NM_001372062.1:c.736-32693C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-242157358-G-A
• chr1-242157358-G-C
• chr1-242157358-G-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.736-32693C>T 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 152,224 control chromosomes in the GnomAD database, including 54,451 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 (54451 hom., cov: 33)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63
• 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]

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLD5	NM_001372062.1	c.736-32693C>T		intron_variant	Intron 5 of 9	ENST00000536534.7	NP_001358991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLD5	ENST00000536534.7	c.736-32693C>T		intron_variant	Intron 5 of 9	1	NM_001372062.1	ENSP00000440896.1

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128049 AN: 152106 Hom.: 54396 Cov.: 33

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.791

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: 128163 AN: 152224 Hom.: 54451 Cov.: 33 AF XY: 0.846 AC XY: 62964 AN XY: 74438

African (AFR) AF: 0.955 AC: 39665 AN: 41548

American (AMR) AF: 0.837 AC: 12804 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2845 AN: 3470

East Asian (EAS) AF: 0.923 AC: 4771 AN: 5170

South Asian (SAS) AF: 0.943 AC: 4547 AN: 4824

European-Finnish (FIN) AF: 0.791 AC: 8387 AN: 10598

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

European-Non Finnish (NFE) AF: 0.771 AC: 52427 AN: 68006

Other (OTH) AF: 0.836 AC: 1761 AN: 2106

Alfa AF: 0.809 Hom.: 5848

Bravo AF: 0.849

Asia WGS AF: 0.917 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.56
PhyloP100		-3.6
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: rs316838; hg19: chr1-242320660;