Variant ENST00000654303.1:n.25_32delGGGGCTCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000654303.1(CA3-AS1):n.25_32delGGGGCTCC 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 0.00266 in 232,476 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0018 ( 6 hom., cov: 0)

Exomes 𝑓: 0.0042 ( 9 hom. )

Consequence

CA3-AS1
ENST00000654303.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.28

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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00177 (259/146666) while in subpopulation SAS AF= 0.0242 (113/4676). AF 95% confidence interval is 0.0206. There are 6 homozygotes in gnomad4. There are 158 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CA3-AS1	ENST00000654303.1 link	n.25_32delGGGGCTCC	non_coding_transcript_exon_variant	Exon 1 of 3
CA3-AS1	ENST00000517697.6 link	n.193+451_193+458delGGGGCTCC	intron_variant	Intron 1 of 2	4
CA3-AS1	ENST00000521761.6 link	n.334+805_334+812delGGGGCTCC	intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.00176

AC:

258

AN:

146580

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00288

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00107

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0241

Gnomad FIN

AF:

0.000203

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000182

Gnomad OTH

AF:

0.000497

GnomAD4 exome

AF:

0.00418

AC:

359

AN:

85810

Hom.:

AF XY:

0.00630

AC XY:

296

AN XY:

47016

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00101

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0219

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000231

Gnomad4 OTH exome

AF:

0.00206

GnomAD4 genome

AF:

0.00177

AC:

259

AN:

146666

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

158

AN XY:

71514

show subpopulations

Gnomad4 AFR

AF:

0.00289

Gnomad4 AMR

AF:

0.00107

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0242

Gnomad4 FIN

AF:

0.000203

Gnomad4 NFE

AF:

0.000182

Gnomad4 OTH

AF:

0.000491

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