12-47338855-A-G

Variant names:

• chr12-47338855-A-G
• rs215340

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 0.814 in 152,140 control chromosomes in the GnomAD database, including 50,798 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 0.81 (50798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.814 AC: 123750 AN: 152022 Hom.: 50760 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.814 AC: 123844 AN: 152140 Hom.: 50798 Cov.: 31 AF XY: 0.814 AC XY: 60557 AN XY: 74392

African (AFR) AF: 0.917 AC: 38045 AN: 41498

American (AMR) AF: 0.770 AC: 11771 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2723 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4903 AN: 5186

South Asian (SAS) AF: 0.765 AC: 3693 AN: 4828

European-Finnish (FIN) AF: 0.802 AC: 8481 AN: 10574

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51639 AN: 67980

Other (OTH) AF: 0.788 AC: 1663 AN: 2110

Alfa AF: 0.775 Hom.: 145396

Bravo AF: 0.819

Asia WGS AF: 0.828 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs215340; hg19: chr12-47732638;