chr1-242358740-A-G

Variant names:

• chr1-242358740-A-G
• rs2919024
• NM_001372062.1:c.190-10498T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001372062.1(PLD5):​c.190-10498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 152,290 control chromosomes in the GnomAD database, including 50 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 0.021 (50 hom., cov: 31)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• 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=-1.08).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0212 (3230/152290) while in subpopulation EAS AF = 0.0326 (169/5180). AF 95% confidence interval is 0.0311. There are 50 homozygotes in GnomAd4. There are 1553 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 50 AR gene

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.190-10498T>C		intron	N/A	NP_001358991.1	Q8N7P1-1
	PLD5	NM_001195811.2		c.4-10498T>C		intron	N/A	NP_001182740.1	Q8N7P1-4
	PLD5	NM_001320272.2		c.-94-10498T>C		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.190-10498T>C		intron	N/A	ENSP00000440896.1	Q8N7P1-1
	PLD5	ENST00000427495.5	TSL:1	c.4-10498T>C		intron	N/A	ENSP00000401285.1	Q8N7P1-4
	PLD5	ENST00000442594.6	TSL:5	c.190-10498T>C		intron	N/A	ENSP00000414188.3	Q8N7P1-1

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3222 AN: 152172 Hom.: 51 Cov.: 31

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0212 AC: 3230 AN: 152290 Hom.: 50 Cov.: 31 AF XY: 0.0209 AC XY: 1553 AN XY: 74452

African (AFR) AF: 0.0326 AC: 1354 AN: 41562

American (AMR) AF: 0.0166 AC: 254 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3468

East Asian (EAS) AF: 0.0326 AC: 169 AN: 5180

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4820

European-Finnish (FIN) AF: 0.00301 AC: 32 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0145 AC: 988 AN: 68024

Other (OTH) AF: 0.0237 AC: 50 AN: 2112

Alfa AF: 0.0193 Hom.: 66

Bravo AF: 0.0235

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.23
PhyloP100		-2.2
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: rs2919024; hg19: chr1-242522042;