rs2789697

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-80136083-C-A
• chr10-80136083-C-G
• chr10-80136083-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001012973.3(PLAC9):​c.64+3257C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAC9	NM_001012973.3	MANE Select	c.64+3257C>A		intron	N/A	NP_001012991.1
	PLAC9	NM_001331125.2		c.64+3257C>A		intron	N/A	NP_001318054.1
	PLAC9	NR_138551.2		n.171+4252C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAC9	ENST00000372263.4	TSL:1 MANE Select	c.64+3257C>A		intron	N/A	ENSP00000361337.3
	PLAC9	ENST00000372267.6	TSL:3	c.64+3257C>A		intron	N/A	ENSP00000361341.2
	PLAC9	ENST00000372270.6	TSL:2	c.-63+4252C>A		intron	N/A	ENSP00000361344.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.13
PhyloP100		-0.43

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;