rs3851052

Variant names:

• chr10-80138439-A-C
• rs3851052
• NM_001012973.3:c.65-3643A>C

Variant summary

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

The NM_001012973.3(PLAC9):​c.65-3643A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,116 control chromosomes in the GnomAD database, including 2,842 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 0.14 (2842 hom., cov: 32)
• Consequence: PLAC9 NM_001012973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLAC9	NM_001012973.3	c.65-3643A>C		intron_variant	Intron 1 of 3	ENST00000372263.4	NP_001012991.1
PLAC9	NM_001331125.2	c.65-3643A>C		intron_variant	Intron 1 of 2		NP_001318054.1
PLAC9	NR_138551.2	n.172-3643A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLAC9	ENST00000372263.4	c.65-3643A>C		intron_variant	Intron 1 of 3	1	NM_001012973.3	ENSP00000361337.3
PLAC9	ENST00000372267.6	c.65-3643A>C		intron_variant	Intron 1 of 2	3		ENSP00000361341.2
PLAC9	ENST00000372270.6	c.-62-3643A>C		intron_variant	Intron 1 of 3	2		ENSP00000361344.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21873 AN: 151998 Hom.: 2836 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0378

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.144 AC: 21917 AN: 152116 Hom.: 2842 Cov.: 32 AF XY: 0.139 AC XY: 10308 AN XY: 74372

African (AFR) AF: 0.350 AC: 14482 AN: 41430

American (AMR) AF: 0.0791 AC: 1209 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0397 AC: 191 AN: 4816

European-Finnish (FIN) AF: 0.0645 AC: 685 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0716 AC: 4868 AN: 68004

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.0906 Hom.: 1006

Bravo AF: 0.156

Asia WGS AF: 0.0380 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		0.13
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: rs3851052; hg19: chr10-81898195;