chr3-26463703-A-G

Position:

• chr3-26463703-A-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26463703A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.338

Alfa AF: 0.314 Hom.: 3515

Bravo AF: 0.327

Asia WGS AF: 0.509 AC: 1767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2366104; hg19: chr3-26505194;