Variant ENST00000654303.1:n.9_32dupGGGGCTCCGGGGCTCCGGGGCTCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000654303.1(CA3-AS1):n.9_32dupGGGGCTCCGGGGCTCCGGGGCTCC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 232,482 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000035 ( 0 hom. )

Consequence

CA3-AS1
ENST00000654303.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00800

Variant links:

Genes affected

CA3-AS1 (HGNC:51657): (CA3 antisense RNA 1)

CA3-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA3-AS1	NR_121630.1 link	n.334+789_334+812dupGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2
CA3-AS1	NR_121631.1 link	n.106+435_106+458dupGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CA3-AS1	ENST00000654303.1 link	n.9_32dupGGGGCTCCGGGGCTCCGGGGCTCC	non_coding_transcript_exon_variant	Exon 1 of 3
CA3-AS1	ENST00000517697.6 link	n.193+435_193+458dupGGGGCTCCGGGGCTCCGGGGCTCC	intron_variant	Intron 1 of 2	4
CA3-AS1	ENST00000521761.6 link	n.334+789_334+812dupGGGGCTCCGGGGCTCCGGGGCTCC	intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.000218

AC:

AN:

146586

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000731

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000133

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000152

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000350

AC:

AN:

85810

Hom.:

AF XY:

0.0000425

AC XY:

AN XY:

47016

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000384

Gnomad4 OTH exome

AF:

0.000206

GnomAD4 genome

AF:

0.000225

AC:

AN:

146672

Hom.:

Cov.:

AF XY:

0.000266

AC XY:

AN XY:

71516

show subpopulations

Gnomad4 AFR

AF:

0.000755

Gnomad4 AMR

AF:

0.000133

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000152

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over