3-12004293-G-T

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 0.756 in 153,652 control chromosomes in the GnomAD database, including 46,413 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 0.76 (45563 hom., cov: 26)
  • Exomes 𝑓: 0.63 (850 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.759 AC: 114193 AN: 150550 Hom.: 45550 Cov.: 26

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.784

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.767

GnomAD4 exome AF: 0.632 AC: 1890 AN: 2990 Hom.: 850 AF XY: 0.649 AC XY: 1051 AN XY: 1620

Gnomad4 AFR exome AF: 0.0804

Gnomad4 AMR exome AF: 0.580

Gnomad4 ASJ exome AF: 0.491

Gnomad4 EAS exome AF: 0.255

Gnomad4 SAS exome AF: 0.958

Gnomad4 FIN exome AF: 0.806

Gnomad4 NFE exome AF: 0.782

Gnomad4 OTH exome AF: 0.605

GnomAD4 genome AF: 0.758 AC: 114248 AN: 150662 Hom.: 45563 Cov.: 26 AF XY: 0.762 AC XY: 56071 AN XY: 73552

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.768

Alfa AF: 0.788 Hom.: 4552

Bravo AF: 0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	2.0
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2623873; hg19: chr3-12045767;