3-26463703-A-G

Variant names:

• chr3-26463703-A-G
• rs2366104

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.326 in 152,016 control chromosomes in the GnomAD database, including 8,485 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 0.33 (8485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49459 AN: 151896 Hom.: 8459 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.326 AC: 49523 AN: 152016 Hom.: 8485 Cov.: 32 AF XY: 0.328 AC XY: 24401 AN XY: 74300

African (AFR) AF: 0.309 AC: 12815 AN: 41464

American (AMR) AF: 0.317 AC: 4847 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3472

East Asian (EAS) AF: 0.667 AC: 3443 AN: 5164

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4814

European-Finnish (FIN) AF: 0.350 AC: 3691 AN: 10544

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20947 AN: 67982

Other (OTH) AF: 0.338 AC: 711 AN: 2106

Alfa AF: 0.313 Hom.: 3927

Bravo AF: 0.327

Asia WGS AF: 0.509 AC: 1767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	19
DANN	Benign	0.88
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs2366104; hg19: chr3-26505194;