12-47619923-A-T

Variant names:

• chr12-47619923-A-T
• rs855272

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 0.491 in 152,006 control chromosomes in the GnomAD database, including 20,403 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 0.49 (20403 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• 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 (EAS) allele frequency at 95% confidence interval = 0.612 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: 0.492 AC: 74656 AN: 151888 Hom.: 20396 Cov.: 30

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.491 AC: 74685 AN: 152006 Hom.: 20403 Cov.: 30 AF XY: 0.493 AC XY: 36654 AN XY: 74294

African (AFR) AF: 0.244 AC: 10137 AN: 41472

American (AMR) AF: 0.448 AC: 6842 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1886 AN: 3472

East Asian (EAS) AF: 0.630 AC: 3248 AN: 5156

South Asian (SAS) AF: 0.576 AC: 2772 AN: 4814

European-Finnish (FIN) AF: 0.639 AC: 6750 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41305 AN: 67940

Other (OTH) AF: 0.488 AC: 1029 AN: 2110

Alfa AF: 0.533 Hom.: 2792

Bravo AF: 0.464

Asia WGS AF: 0.547 AC: 1901 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	0.28
DANN	Benign	0.43
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs855272; hg19: chr12-48013706;