Variant ENST00000654303.1:n.25_32dupGGGGCTCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000654303.1(CA3-AS1):n.25_32dupGGGGCTCC 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 0.502 in 231,744 control chromosomes in the GnomAD database, including 33,341 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 24746 hom., cov: 0)

Exomes 𝑓: 0.38 ( 8595 hom. )

Consequence

CA3-AS1
ENST00000654303.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00800

Variant links:

Genes affected

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

CA3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 8-85463769-A-AGGAGCCCC is Benign according to our data. Variant chr8-85463769-A-AGGAGCCCC is described in ClinVar as [Benign]. Clinvar id is 1225462.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA3-AS1	NR_121630.1 link	n.334+805_334+812dupGGGGCTCC		intron_variant	Intron 1 of 2
CA3-AS1	NR_121631.1 link	n.106+451_106+458dupGGGGCTCC		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CA3-AS1	ENST00000654303.1 link	n.25_32dupGGGGCTCC	non_coding_transcript_exon_variant	Exon 1 of 3
CA3-AS1	ENST00000517697.6 link	n.193+451_193+458dupGGGGCTCC	intron_variant	Intron 1 of 2	4
CA3-AS1	ENST00000521761.6 link	n.334+805_334+812dupGGGGCTCC	intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

84047

AN:

146442

Hom.:

24730

Cov.:

show subpopulations

Gnomad AFR

AF:

0.633

Gnomad AMI

AF:

0.497

Gnomad AMR

AF:

0.524

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.638

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.587

GnomAD4 exome

AF:

0.380

AC:

32354

AN:

85216

Hom.:

8595

AF XY:

0.367

AC XY:

17148

AN XY:

46706

show subpopulations

Gnomad4 AFR exome

AF:

0.356

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.306

Gnomad4 EAS exome

AF:

0.0666

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.483

Gnomad4 NFE exome

AF:

0.424

Gnomad4 OTH exome

AF:

0.382

GnomAD4 genome

AF:

0.574

AC:

84090

AN:

146528

Hom.:

24746

Cov.:

AF XY:

0.576

AC XY:

41147

AN XY:

71450

show subpopulations

Gnomad4 AFR

AF:

0.632

Gnomad4 AMR

AF:

0.524

Gnomad4 ASJ

AF:

0.557

Gnomad4 EAS

AF:

0.387

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.693

Gnomad4 NFE

AF:

0.560

Gnomad4 OTH

AF:

0.587

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 11, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over