12-91113176-T-G

Variant names:

• chr12-91113176-T-G
• rs3759222

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 0.719 in 152,060 control chromosomes in the GnomAD database, including 42,815 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 0.72 (42815 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 8 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 (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109291 AN: 151944 Hom.: 42811 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.719 AC: 109317 AN: 152060 Hom.: 42815 Cov.: 33 AF XY: 0.723 AC XY: 53759 AN XY: 74334

African (AFR) AF: 0.377 AC: 15617 AN: 41472

American (AMR) AF: 0.796 AC: 12148 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2773 AN: 3468

East Asian (EAS) AF: 0.678 AC: 3498 AN: 5156

South Asian (SAS) AF: 0.847 AC: 4078 AN: 4814

European-Finnish (FIN) AF: 0.910 AC: 9647 AN: 10602

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59040 AN: 67964

Other (OTH) AF: 0.755 AC: 1597 AN: 2116

Alfa AF: 0.801 Hom.: 92284

Bravo AF: 0.693

Asia WGS AF: 0.721 AC: 2492 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs3759222; hg19: chr12-91506953;