12-106987782-T-A

Variant names:

• chr12-106987782-T-A
• rs10861683

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 0.267 in 152,018 control chromosomes in the GnomAD database, including 5,921 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 0.27 (5921 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 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: 0.267 AC: 40627 AN: 151900 Hom.: 5920 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.267 AC: 40638 AN: 152018 Hom.: 5921 Cov.: 31 AF XY: 0.264 AC XY: 19592 AN XY: 74306

African (AFR) AF: 0.150 AC: 6214 AN: 41462

American (AMR) AF: 0.268 AC: 4093 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1453 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4814

European-Finnish (FIN) AF: 0.266 AC: 2810 AN: 10554

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23262 AN: 67950

Other (OTH) AF: 0.306 AC: 645 AN: 2110

Alfa AF: 0.171 Hom.: 349

Bravo AF: 0.263

Asia WGS AF: 0.270 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.76
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs10861683; hg19: chr12-107381560;