8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCCGGAGCCCC

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)
CA2 (HGNC:1373): (carbonic anhydrase 2) The protein encoded by this gene is one of several isozymes of carbonic anhydrase, which catalyzes reversible hydration of carbon dioxide. Defects in this enzyme are associated with osteopetrosis and renal tubular acidosis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]

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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-AS1NR_121630.1 linkn.334+805_334+812delGGGGCTCC intron_variant Intron 1 of 2
CA3-AS1NR_121631.1 linkn.106+451_106+458delGGGGCTCC intron_variant Intron 1 of 2
CA2NM_000067.3 linkc.-312_-305delGGAGCCCC upstream_gene_variant ENST00000285379.10 NP_000058.1 P00918V9HW21
CA2NM_001293675.2 linkc.-496_-489delGGAGCCCC upstream_gene_variant NP_001280604.1 V9HW21

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA2ENST00000285379.10 linkc.-312_-305delGGAGCCCC upstream_gene_variant 1 NM_000067.3 ENSP00000285379.4 P00918

Frequencies

GnomAD3 genomes
AF:
0.00176
AC:
258
AN:
146580
Hom.:
6
Cov.:
0
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.:
9
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.:
6
Cov.:
0
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.

Other links and lift over

dbSNP: rs77895131; hg19: chr8-86375998; API