3-12681371-A-G

Position:

• chr3-12681371-A-G

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 0.493 in 151,944 control chromosomes in the GnomAD database, including 19,289 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 0.49 (19289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74870 AN: 151826 Hom.: 19288 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.493 AC: 74909 AN: 151944 Hom.: 19289 Cov.: 32 AF XY: 0.497 AC XY: 36925 AN XY: 74238

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.495

Alfa AF: 0.518 Hom.: 40841

Bravo AF: 0.481

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6442323; hg19: chr3-12722870;