rs77895131

Variant names:

• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-A
• rs77895131
• ENST00000654303.1:n.9_32delGGGGCTCCGGGGCTCCGGGGCTCC

Your query was ambiguous. Multiple possible variants found:

• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-A
• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCC
• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCCGGAGCCCC
• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC
• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC
• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC
• chr8-85463769-AGGAGCCCCGGAGCCCCGGAGCCCC-AGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCCGGAGCCCC

Variant summary

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

The ENST00000654303.1(CA3-AS1):​n.9_32delGGGGCTCCGGGGCTCCGGGGCTCC 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 0.0000387 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 0.000027 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000058 (0 hom.)
• Consequence: CA3-AS1 ENST00000654303.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.28

Genes affected

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

ACMG classification

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	n.334+789_334+812delGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2
CA3-AS1	NR_121631.1	n.106+435_106+458delGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA3-AS1	ENST00000654303.1	n.9_32delGGGGCTCCGGGGCTCCGGGGCTCC		non_coding_transcript_exon_variant	Exon 1 of 3
CA3-AS1	ENST00000517697.6	n.193+435_193+458delGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2	4
CA3-AS1	ENST00000521761.6	n.334+789_334+812delGGGGCTCCGGGGCTCCGGGGCTCC		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0000273 AC: 4 AN: 146586 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000854

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000583 AC: 5 AN: 85810 Hom.: 0 AF XY: 0.0000851 AC XY: 4 AN XY: 47016

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: 0.000327

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000273 AC: 4 AN: 146672 Hom.: 0 Cov.: 0 AF XY: 0.0000280 AC XY: 2 AN XY: 71516

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000855

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77895131; hg19: chr8-86375998;