3-12681371-A-G

Variant names:

• chr3-12681371-A-G
• rs6442323

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;