rs3762097

Variant names:

• chr10-80141619-C-A
• rs3762097
• NM_001012973.3:c.65-463C>A

Variant summary

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

The NM_001012973.3(PLAC9):​c.65-463C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,700 control chromosomes in the GnomAD database, including 11,372 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 (11372 hom., cov: 31)
• Consequence: PLAC9 NM_001012973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012973.3. 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
	PLAC9	NM_001012973.3	MANE Select	c.65-463C>A		intron	N/A	NP_001012991.1	Q5JTB6
	PLAC9	NM_001331125.2		c.65-463C>A		intron	N/A	NP_001318054.1	Q5JTB5
	PLAC9	NR_138551.2		n.172-463C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAC9	ENST00000372263.4	TSL:1 MANE Select	c.65-463C>A		intron	N/A	ENSP00000361337.3	Q5JTB6
	PLAC9	ENST00000941179.1		c.65-463C>A		intron	N/A	ENSP00000611238.1
	PLAC9	ENST00000372267.6	TSL:3	c.65-463C>A		intron	N/A	ENSP00000361341.2	Q5JTB5

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56227 AN: 151582 Hom.: 11373 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.371 AC: 56221 AN: 151700 Hom.: 11372 Cov.: 31 AF XY: 0.373 AC XY: 27661 AN XY: 74092

African (AFR) AF: 0.196 AC: 8125 AN: 41382

American (AMR) AF: 0.426 AC: 6488 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3464

East Asian (EAS) AF: 0.548 AC: 2821 AN: 5146

South Asian (SAS) AF: 0.371 AC: 1775 AN: 4784

European-Finnish (FIN) AF: 0.455 AC: 4780 AN: 10496

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29489 AN: 67872

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.265 Hom.: 678

Bravo AF: 0.361

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		-0.73
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: rs3762097; hg19: chr10-81901375;