10-80136083-C-G

Variant names:

• chr10-80136083-C-G
• rs2789697
• NM_001012973.3:c.64+3257C>G

Variant summary

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

The NM_001012973.3(PLAC9):​c.64+3257C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,086 control chromosomes in the GnomAD database, including 11,567 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 0.37 (11567 hom., cov: 32)
• Consequence: PLAC9 NM_001012973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 1 publications found

Genes affected

PLAC9 (HGNC:19255): (placenta associated 9) Predicted to be located in extracellular region. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLAC9	NM_001012973.3	c.64+3257C>G		intron_variant	Intron 1 of 3	ENST00000372263.4	NP_001012991.1
PLAC9	NM_001331125.2	c.64+3257C>G		intron_variant	Intron 1 of 2		NP_001318054.1
PLAC9	NR_138551.2	n.171+4252C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLAC9	ENST00000372263.4	c.64+3257C>G		intron_variant	Intron 1 of 3	1	NM_001012973.3	ENSP00000361337.3
PLAC9	ENST00000372267.6	c.64+3257C>G		intron_variant	Intron 1 of 2	3		ENSP00000361341.2
PLAC9	ENST00000372270.6	c.-63+4252C>G		intron_variant	Intron 1 of 3	2		ENSP00000361344.1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56797 AN: 151968 Hom.: 11564 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.373 AC: 56800 AN: 152086 Hom.: 11567 Cov.: 32 AF XY: 0.374 AC XY: 27833 AN XY: 74346

African (AFR) AF: 0.201 AC: 8336 AN: 41510

American (AMR) AF: 0.422 AC: 6451 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2729 AN: 5160

South Asian (SAS) AF: 0.329 AC: 1588 AN: 4824

European-Finnish (FIN) AF: 0.460 AC: 4865 AN: 10566

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30067 AN: 67968

Other (OTH) AF: 0.383 AC: 806 AN: 2106

Alfa AF: 0.388 Hom.: 1506

Bravo AF: 0.365

Asia WGS AF: 0.391 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.22
PhyloP100		-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: rs2789697; hg19: chr10-81895839;