rs12263945

Variant names:

• chr10-121082016-A-G
• rs12263945

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 0.166 in 152,166 control chromosomes in the GnomAD database, including 2,700 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 (2700 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25269 AN: 152048 Hom.: 2696 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.166 AC: 25305 AN: 152166 Hom.: 2700 Cov.: 33 AF XY: 0.173 AC XY: 12870 AN XY: 74400

African (AFR) AF: 0.261 AC: 10828 AN: 41494

American (AMR) AF: 0.255 AC: 3899 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.164 AC: 851 AN: 5174

South Asian (SAS) AF: 0.311 AC: 1495 AN: 4808

European-Finnish (FIN) AF: 0.136 AC: 1437 AN: 10602

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0909 AC: 6183 AN: 68004

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.137 Hom.: 235

Bravo AF: 0.174

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12263945; hg19: chr10-122841529;