12-91113176-T-G

Variant names:

• chr12-91113176-T-G
• rs3759222

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.755

Alfa AF: 0.839 Hom.: 60043

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759222; hg19: chr12-91506953;