rs3759223

Variant names:

• chr12-91113006-A-G
• rs3759223

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 0.0312 in 152,248 control chromosomes in the GnomAD database, including 248 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 0.031 (248 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 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: 0.0312 AC: 4752 AN: 152128 Hom.: 247 Cov.: 33

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0185

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0312 AC: 4757 AN: 152248 Hom.: 248 Cov.: 33 AF XY: 0.0344 AC XY: 2564 AN XY: 74434

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0185

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.0907

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0248 Hom.: 13

Bravo AF: 0.0323

Asia WGS AF: 0.168 AC: 578 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759223; hg19: chr12-91506783;