chr12-63171397-G-A

Variant names:

• chr12-63171397-G-A
• rs11832266

Variant summary

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

The variant allele was found at a frequency of 0.17 in 152,032 control chromosomes in the GnomAD database, including 5,012 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 0.17 (5012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25857 AN: 151914 Hom.: 4990 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.170 AC: 25913 AN: 152032 Hom.: 5012 Cov.: 32 AF XY: 0.168 AC XY: 12498 AN XY: 74328

African (AFR) AF: 0.476 AC: 19726 AN: 41410

American (AMR) AF: 0.0800 AC: 1222 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.110 AC: 567 AN: 5160

South Asian (SAS) AF: 0.158 AC: 760 AN: 4816

European-Finnish (FIN) AF: 0.0551 AC: 584 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2627 AN: 67990

Other (OTH) AF: 0.139 AC: 294 AN: 2114

Alfa AF: 0.123 Hom.: 552

Bravo AF: 0.183

Asia WGS AF: 0.171 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.49
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11832266; hg19: chr12-63565177;