3-12446151-G-T

Variant names:

• chr3-12446151-G-T
• rs6806708

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 0.346 in 152,008 control chromosomes in the GnomAD database, including 10,252 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 0.35 (10252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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: 0.346 AC: 52560 AN: 151890 Hom.: 10247 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.346 AC: 52616 AN: 152008 Hom.: 10252 Cov.: 32 AF XY: 0.343 AC XY: 25491 AN XY: 74304

African (AFR) AF: 0.522 AC: 21622 AN: 41446

American (AMR) AF: 0.338 AC: 5166 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3468

East Asian (EAS) AF: 0.0270 AC: 140 AN: 5184

South Asian (SAS) AF: 0.203 AC: 978 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3269 AN: 10540

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18979 AN: 67954

Other (OTH) AF: 0.317 AC: 668 AN: 2106

Alfa AF: 0.292 Hom.: 8208

Bravo AF: 0.360

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.061
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6806708; hg19: chr3-12487650;