chr8-85462435-A-G

Position:

• chr8-85462435-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524052.2(CA3-AS1):​n.417+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 ENST00000524052.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

Genes affected

CA3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CA3-AS1	NR_121630.1	n.400+301T>C		intron_variant
CA3-AS1	NR_121631.1	n.172+301T>C		intron_variant
CA3-AS1	NR_121632.1	n.189+301T>C		intron_variant
CA3-AS1	NR_121633.1	n.189+301T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CA3-AS1	ENST00000517697.6	n.259+301T>C		intron_variant		4
CA3-AS1	ENST00000521761.6	n.400+301T>C		intron_variant		4
CA3-AS1	ENST00000524052.2	n.417+301T>C		intron_variant		2

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

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.710

Alfa AF: 0.677 Hom.: 5182

Bravo AF: 0.691

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758078; hg19: chr8-86374664;