rs3762097

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLAC9	NM_001012973.3	c.65-463C>A		intron_variant	Intron 1 of 3	ENST00000372263.4	NP_001012991.1
PLAC9	NM_001331125.2	c.65-463C>A		intron_variant	Intron 1 of 2		NP_001318054.1
PLAC9	NR_138551.2	n.172-463C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLAC9	ENST00000372263.4	c.65-463C>A		intron_variant	Intron 1 of 3	1	NM_001012973.3	ENSP00000361337.3
PLAC9	ENST00000372267.6	c.65-463C>A		intron_variant	Intron 1 of 2	3		ENSP00000361341.2
PLAC9	ENST00000372270.6	c.-62-463C>A		intron_variant	Intron 1 of 3	2		ENSP00000361344.1

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.389

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.28

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762097; hg19: chr10-81901375;