rs12447341

Variant names:

• chr16-68839783-T-C
• rs12447341

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 0.622 in 152,030 control chromosomes in the GnomAD database, including 29,449 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 0.62 (29449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.622 AC: 94468 AN: 151912 Hom.: 29408 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.622 AC: 94574 AN: 152030 Hom.: 29449 Cov.: 32 AF XY: 0.622 AC XY: 46182 AN XY: 74290

African (AFR) AF: 0.620 AC: 25716 AN: 41448

American (AMR) AF: 0.658 AC: 10058 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3631 AN: 5168

South Asian (SAS) AF: 0.651 AC: 3140 AN: 4824

European-Finnish (FIN) AF: 0.569 AC: 6007 AN: 10554

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41905 AN: 67970

Other (OTH) AF: 0.634 AC: 1341 AN: 2114

Alfa AF: 0.616 Hom.: 4360

Bravo AF: 0.629

Asia WGS AF: 0.724 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12447341; hg19: chr16-68873686;