rs6546366

Variant names:

• chr2-68262535-A-C
• rs6546366
• ENST00000687213.2:n.187+10801A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-68262535-A-C
• chr2-68262535-A-T

Variant summary

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

The ENST00000687213.2(PPP3R1-AS1):​n.187+10801A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,080 control chromosomes in the GnomAD database, including 43,113 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 0.74 (43113 hom., cov: 33)
• Consequence: PPP3R1-AS1 ENST00000687213.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 7 publications found

Genes affected

PPP3R1-AS1 (HGNC:58298):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687213.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP3R1-AS1	ENST00000687213.2		n.187+10801A>C		intron	N/A
	PPP3R1-AS1	ENST00000702914.1		n.132+10801A>C		intron	N/A
	PPP3R1-AS1	ENST00000702987.2		n.102+10886A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112984 AN: 151962 Hom.: 43042 Cov.: 33

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.744 AC: 113113 AN: 152080 Hom.: 43113 Cov.: 33 AF XY: 0.743 AC XY: 55199 AN XY: 74330

African (AFR) AF: 0.932 AC: 38697 AN: 41536

American (AMR) AF: 0.720 AC: 10997 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2464 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3436 AN: 5184

South Asian (SAS) AF: 0.772 AC: 3726 AN: 4828

European-Finnish (FIN) AF: 0.683 AC: 7203 AN: 10542

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44144 AN: 67934

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.713 Hom.: 5225

Bravo AF: 0.753

Asia WGS AF: 0.768 AC: 2634 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.47
PhyloP100		-0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6546366;

hg19: chr2-68489667;