8-85462435-A-G

Variant names:

• chr8-85462435-A-G
• rs3758078
• ENST00000517697.7:n.259+301T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524052.3(CA3-AS1):​n.616+301T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,124 control chromosomes in the GnomAD database, including 37,148 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (37148 hom., cov: 33)
• Consequence: CA3-AS1 ENST00000524052.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524052.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA3-AS1	NR_121630.1		n.400+301T>C		intron	N/A
	CA3-AS1	NR_121631.1		n.172+301T>C		intron	N/A
	CA3-AS1	NR_121632.1		n.189+301T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA3-AS1	ENST00000517697.7	TSL:4	n.259+301T>C		intron	N/A
	CA3-AS1	ENST00000521761.6	TSL:4	n.400+301T>C		intron	N/A
	CA3-AS1	ENST00000524052.3	TSL:2	n.616+301T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104739 AN: 152006 Hom.: 37104 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.705

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.689 AC: 104835 AN: 152124 Hom.: 37148 Cov.: 33 AF XY: 0.687 AC XY: 51047 AN XY: 74358

African (AFR) AF: 0.847 AC: 35167 AN: 41522

American (AMR) AF: 0.605 AC: 9231 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5174

South Asian (SAS) AF: 0.496 AC: 2395 AN: 4826

European-Finnish (FIN) AF: 0.734 AC: 7761 AN: 10580

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43402 AN: 67970

Other (OTH) AF: 0.710 AC: 1498 AN: 2110

Alfa AF: 0.681 Hom.: 5438

Bravo AF: 0.691

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.53
PhyloP100		-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3758078;

hg19: chr8-86374664;