chr12-63522902-G-A

Position:

• chr12-63522902-G-A

Variant summary

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

The variant allele was found at a frequency of 0.299 in 151,890 control chromosomes in the GnomAD database, including 8,996 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 0.30 (8996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45334 AN: 151772 Hom.: 8951 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.299 AC: 45435 AN: 151890 Hom.: 8996 Cov.: 32 AF XY: 0.295 AC XY: 21865 AN XY: 74188

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.262

Alfa AF: 0.196 Hom.: 6700

Bravo AF: 0.320

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1603810; hg19: chr12-63916682;