rs12097667

Variant names:

• chr1-242384646-C-A
• rs12097667
• NM_001372062.1:c.190-36404G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-242384646-C-A
• chr1-242384646-C-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.190-36404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,144 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• 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]

LOC100421344 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 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.190-36404G>T		intron	N/A	NP_001358991.1	Q8N7P1-1
	PLD5	NM_001195811.2		c.4-36404G>T		intron	N/A	NP_001182740.1	Q8N7P1-4
	PLD5	NM_001320272.2		c.-94-36404G>T		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.190-36404G>T		intron	N/A	ENSP00000440896.1	Q8N7P1-1
	PLD5	ENST00000427495.5	TSL:1	c.4-36404G>T		intron	N/A	ENSP00000401285.1	Q8N7P1-4
	PLD5	ENST00000442594.6	TSL:5	c.190-36404G>T		intron	N/A	ENSP00000414188.3	Q8N7P1-1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25871 AN: 152026 Hom.: 2410 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.170 AC: 25910 AN: 152144 Hom.: 2409 Cov.: 32 AF XY: 0.172 AC XY: 12797 AN XY: 74384

African (AFR) AF: 0.202 AC: 8380 AN: 41494

American (AMR) AF: 0.251 AC: 3833 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3466

East Asian (EAS) AF: 0.189 AC: 979 AN: 5170

South Asian (SAS) AF: 0.0736 AC: 355 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1853 AN: 10576

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9419 AN: 68012

Other (OTH) AF: 0.167 AC: 354 AN: 2116

Alfa AF: 0.148 Hom.: 4147

Bravo AF: 0.182

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.97
DANN	Benign	0.37
PhyloP100		0.010
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: rs12097667; hg19: chr1-242547948;