3-186775524-T-G

Variant names:

• chr3-186775524-T-G
• rs266733

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 0.441 in 151,828 control chromosomes in the GnomAD database, including 15,378 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 0.44 (15378 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 7 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 (AMR) allele frequency at 95% confidence interval = 0.469 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: 0.441 AC: 66954 AN: 151710 Hom.: 15377 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.441 AC: 66980 AN: 151828 Hom.: 15378 Cov.: 31 AF XY: 0.448 AC XY: 33227 AN XY: 74186

African (AFR) AF: 0.334 AC: 13828 AN: 41392

American (AMR) AF: 0.476 AC: 7268 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2191 AN: 5146

South Asian (SAS) AF: 0.422 AC: 2033 AN: 4820

European-Finnish (FIN) AF: 0.642 AC: 6762 AN: 10540

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32125 AN: 67898

Other (OTH) AF: 0.407 AC: 857 AN: 2106

Alfa AF: 0.471 Hom.: 2331

Bravo AF: 0.421

Asia WGS AF: 0.442 AC: 1538 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	1.7
DANN	Benign	0.52
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs266733; hg19: chr3-186493313;