chr3-12447843-T-G

Variant names:

• chr3-12447843-T-G
• rs17819328

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.38 in 151,996 control chromosomes in the GnomAD database, including 12,700 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 0.38 (12700 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.380 AC: 57777 AN: 151878 Hom.: 12703 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.380 AC: 57787 AN: 151996 Hom.: 12700 Cov.: 31 AF XY: 0.388 AC XY: 28827 AN XY: 74272

African (AFR) AF: 0.201 AC: 8326 AN: 41454

American (AMR) AF: 0.382 AC: 5838 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4718 AN: 5174

South Asian (SAS) AF: 0.621 AC: 2993 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5061 AN: 10528

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28618 AN: 67954

Other (OTH) AF: 0.365 AC: 770 AN: 2110

Alfa AF: 0.414 Hom.: 28821

Bravo AF: 0.364

Asia WGS AF: 0.628 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs17819328; hg19: chr3-12489342;