chr12-84745301-A-G

Variant names:

• chr12-84745301-A-G
• rs3922762

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 0.629 in 152,078 control chromosomes in the GnomAD database, including 31,510 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 0.63 (31510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95686 AN: 151960 Hom.: 31505 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.629 AC: 95717 AN: 152078 Hom.: 31510 Cov.: 33 AF XY: 0.635 AC XY: 47204 AN XY: 74334

African (AFR) AF: 0.427 AC: 17728 AN: 41500

American (AMR) AF: 0.765 AC: 11663 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2671 AN: 3470

East Asian (EAS) AF: 0.642 AC: 3312 AN: 5158

South Asian (SAS) AF: 0.637 AC: 3075 AN: 4826

European-Finnish (FIN) AF: 0.740 AC: 7836 AN: 10596

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47098 AN: 67962

Other (OTH) AF: 0.680 AC: 1438 AN: 2116

Alfa AF: 0.673 Hom.: 94452

Bravo AF: 0.625

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.66
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3922762; hg19: chr12-85139080;