rs940611

Variant names:

• chr11-63488969-C-G
• rs940611
• NM_001146729.2:c.247G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-63488969-C-G
• chr11-63488969-C-T

Variant summary

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

The NM_001146729.2(PLAAT5):​c.247G>C​(p.Ala83Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 1,606,038 control chromosomes in the GnomAD database, including 14,134 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (6492 hom., cov: 32)
  • Exomes 𝑓: 0.060 (7642 hom.)
• Consequence: PLAAT5 NM_001146729.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 14 publications found

Genes affected

PLAAT5 (HGNC:24978): (phospholipase A and acyltransferase 5) Enables N-acyltransferase activity; phospholipase A1 activity; and phospholipase A2 activity. Acts upstream of or within N-acylphosphatidylethanolamine metabolic process. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [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 (MetaRNN=1.247038E-5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146729.2. 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
	PLAAT5	NM_001146729.2	MANE Select	c.247G>C	p.Ala83Pro	missense	Exon 3 of 6	NP_001140201.2
	PLAAT5	NM_054108.4		c.277G>C	p.Ala93Pro	missense	Exon 3 of 6	NP_473449.2
	PLAAT5	NM_001146728.2		c.277G>C	p.Ala93Pro	missense	Exon 3 of 6	NP_001140200.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAAT5	ENST00000540857.6	TSL:1 MANE Select	c.247G>C	p.Ala83Pro	missense	Exon 3 of 6	ENSP00000444809.1
	PLAAT5	ENST00000301790.4	TSL:1	c.277G>C	p.Ala93Pro	missense	Exon 3 of 6	ENSP00000301790.4
	PLAAT5	ENST00000539221.5	TSL:1	c.277G>C	p.Ala93Pro	missense	Exon 3 of 6	ENSP00000443873.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28889 AN: 151852 Hom.: 6462 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0921

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.143

GnomAD2 exomes AF: 0.0860 AC: 21511 AN: 250200 AF XY: 0.0747

Gnomad AFR exome AF: 0.556

Gnomad AMR exome AF: 0.0471

Gnomad ASJ exome AF: 0.0662

Gnomad EAS exome AF: 0.162

Gnomad FIN exome AF: 0.0472

Gnomad NFE exome AF: 0.0421

Gnomad OTH exome AF: 0.0653

GnomAD4 exome AF: 0.0595 AC: 86562 AN: 1454068 Hom.: 7642 Cov.: 27 AF XY: 0.0568 AC XY: 41127 AN XY: 723830

African (AFR) AF: 0.570 AC: 18830 AN: 33024

American (AMR) AF: 0.0523 AC: 2326 AN: 44492

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 1614 AN: 26044

East Asian (EAS) AF: 0.166 AC: 6561 AN: 39574

South Asian (SAS) AF: 0.0331 AC: 2841 AN: 85798

European-Finnish (FIN) AF: 0.0462 AC: 2466 AN: 53372

Middle Eastern (MID) AF: 0.0661 AC: 380 AN: 5750

European-Non Finnish (NFE) AF: 0.0422 AC: 46625 AN: 1105960

Other (OTH) AF: 0.0819 AC: 4919 AN: 60054

GnomAD4 genome AF: 0.191 AC: 28964 AN: 151970 Hom.: 6492 Cov.: 32 AF XY: 0.186 AC XY: 13832 AN XY: 74306

African (AFR) AF: 0.546 AC: 22571 AN: 41344

American (AMR) AF: 0.0919 AC: 1406 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 226 AN: 3468

East Asian (EAS) AF: 0.157 AC: 813 AN: 5166

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4826

European-Finnish (FIN) AF: 0.0525 AC: 555 AN: 10572

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0423 AC: 2879 AN: 67988

Other (OTH) AF: 0.141 AC: 297 AN: 2108

Alfa AF: 0.0669 Hom.: 860

Bravo AF: 0.210

TwinsUK AF: 0.0426 AC: 158

ALSPAC AF: 0.0426 AC: 164

ESP6500AA AF: 0.525 AC: 2309

ESP6500EA AF: 0.0468 AC: 402

ExAC AF: 0.0944 AC: 11466

Asia WGS AF: 0.103 AC: 358 AN: 3478

EpiCase AF: 0.0416

EpiControl AF: 0.0423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.75	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.24
DANN	Benign	0.099
DEOGEN2	Benign	0.0012	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0030	N
LIST_S2	Benign	0.17	T
MetaRNN	Benign	0.000012	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-0.90	N
PhyloP100		-0.43
PrimateAI	Benign	0.30	T
PROVEAN	Benign	0.85	N
REVEL	Benign	0.047
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.073
MPC		0.16
ClinPred		0.00026	T
GERP RS		-1.0
Varity_R		0.063
gMVP		0.43
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: rs940611; hg19: chr11-63256441; COSMIC: COSV57137156;