rs906114

Variant names:

• chr12-30333330-A-G
• rs906114

Your query was ambiguous. Multiple possible variants found:

• chr12-30333330-A-G
• chr12-30333330-A-T

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 0.232 in 152,092 control chromosomes in the GnomAD database, including 5,056 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 0.23 (5056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.232 AC: 35209 AN: 151974 Hom.: 5049 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.232 AC: 35253 AN: 152092 Hom.: 5056 Cov.: 32 AF XY: 0.232 AC XY: 17218 AN XY: 74340

African (AFR) AF: 0.413 AC: 17133 AN: 41466

American (AMR) AF: 0.183 AC: 2801 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1122 AN: 5180

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4814

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10566

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9955 AN: 67992

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.205 Hom.: 712

Bravo AF: 0.241

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs906114; hg19: chr12-30486263;