6-46704715-TAATC-T

Variant names:

• chr6-46704715-TAATC-T
• rs148052037
• NM_005084.4:c.1190-23_1190-20delGATT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005084.4(PLA2G7):​c.1190-23_1190-20delGATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,467,096 control chromosomes in the GnomAD database, including 102,008 homozygotes. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.30 (8581 hom., cov: 17)
  • Exomes 𝑓: 0.37 (93427 hom.)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.72
• Publications: 5 publications found

Genes affected

PLA2G7 (HGNC:9040): (phospholipase A2 group VII) The protein encoded by this gene is a secreted enzyme that catalyzes the degradation of platelet-activating factor to biologically inactive products. Defects in this gene are a cause of platelet-activating factor acetylhydrolase deficiency. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2009]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 6-46704715-TAATC-T is Benign according to our data. Variant chr6-46704715-TAATC-T is described in ClinVar as [Benign]. Clinvar id is 1252749.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.1190-23_1190-20delGATT		intron_variant	Intron 11 of 11	ENST00000274793.12	NP_005075.3
PLA2G7	NM_001168357.2	c.1190-23_1190-20delGATT		intron_variant	Intron 11 of 11		NP_001161829.1
PLA2G7	XM_005249408.5	c.1190-23_1190-20delGATT		intron_variant	Intron 11 of 11		XP_005249465.1
PLA2G7	XM_047419359.1	c.1055-23_1055-20delGATT		intron_variant	Intron 10 of 10		XP_047275315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12	c.1190-23_1190-20delGATT		intron_variant	Intron 11 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.1190-23_1190-20delGATT		intron_variant	Intron 11 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45603 AN: 151630 Hom.: 8577 Cov.: 17

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.295

GnomAD2 exomes AF: 0.351 AC: 86828 AN: 247356 AF XY: 0.347

Gnomad AFR exome AF: 0.0673

Gnomad AMR exome AF: 0.359

Gnomad ASJ exome AF: 0.300

Gnomad EAS exome AF: 0.573

Gnomad FIN exome AF: 0.391

Gnomad NFE exome AF: 0.393

Gnomad OTH exome AF: 0.335

GnomAD4 exome AF: 0.367 AC: 482785 AN: 1315348 Hom.: 93427 AF XY: 0.364 AC XY: 240880 AN XY: 662240

African (AFR) AF: 0.0613 AC: 1942 AN: 31674

American (AMR) AF: 0.354 AC: 15651 AN: 44194

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 7695 AN: 25294

East Asian (EAS) AF: 0.512 AC: 19875 AN: 38814

South Asian (SAS) AF: 0.198 AC: 16624 AN: 83830

European-Finnish (FIN) AF: 0.393 AC: 20803 AN: 52890

Middle Eastern (MID) AF: 0.219 AC: 1199 AN: 5484

European-Non Finnish (NFE) AF: 0.388 AC: 379620 AN: 977486

Other (OTH) AF: 0.348 AC: 19376 AN: 55682

GnomAD4 genome AF: 0.301 AC: 45615 AN: 151748 Hom.: 8581 Cov.: 17 AF XY: 0.301 AC XY: 22303 AN XY: 74114

African (AFR) AF: 0.0769 AC: 3193 AN: 41530

American (AMR) AF: 0.326 AC: 4972 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1087 AN: 3464

East Asian (EAS) AF: 0.560 AC: 2871 AN: 5130

South Asian (SAS) AF: 0.206 AC: 991 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4034 AN: 10484

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27524 AN: 67772

Other (OTH) AF: 0.292 AC: 617 AN: 2110

Alfa AF: 0.351 Hom.: 1900

Bravo AF: 0.290

Asia WGS AF: 0.327 AC: 1133 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 19, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7
BranchPoint Hunter		5.0
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: rs148052037; hg19: chr6-46672452; COSMIC: COSV51259077; COSMIC: COSV51259077;