3-44202115-G-T

Variant names:

• chr3-44202115-G-T
• rs6808448

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 0.447 in 152,006 control chromosomes in the GnomAD database, including 16,700 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 0.45 (16700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67931 AN: 151888 Hom.: 16688 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.447 AC: 67973 AN: 152006 Hom.: 16700 Cov.: 32 AF XY: 0.456 AC XY: 33916 AN XY: 74304

African (AFR) AF: 0.269 AC: 11128 AN: 41440

American (AMR) AF: 0.540 AC: 8249 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4185 AN: 5182

South Asian (SAS) AF: 0.702 AC: 3383 AN: 4822

European-Finnish (FIN) AF: 0.506 AC: 5346 AN: 10562

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32291 AN: 67934

Other (OTH) AF: 0.449 AC: 950 AN: 2114

Alfa AF: 0.450 Hom.: 3826

Bravo AF: 0.440

Asia WGS AF: 0.715 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.33
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6808448; hg19: chr3-44243607;