3-12277559-A-G

Variant names:

• chr3-12277559-A-G
• rs2920499

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 0.456 in 152,014 control chromosomes in the GnomAD database, including 16,577 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 0.46 (16577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.456 AC: 69246 AN: 151896 Hom.: 16571 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.456 AC: 69280 AN: 152014 Hom.: 16577 Cov.: 32 AF XY: 0.462 AC XY: 34322 AN XY: 74292

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.429

Alfa AF: 0.453 Hom.: 15438

Bravo AF: 0.442

Asia WGS AF: 0.670 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2920499; hg19: chr3-12319058;