3-22606600-G-A

Variant names:

• chr3-22606600-G-A
• rs1349282

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 0.499 in 152,054 control chromosomes in the GnomAD database, including 20,645 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 0.50 (20645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• 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 (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75723 AN: 151936 Hom.: 20605 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.499 AC: 75813 AN: 152054 Hom.: 20645 Cov.: 32 AF XY: 0.494 AC XY: 36691 AN XY: 74310

African (AFR) AF: 0.732 AC: 30357 AN: 41492

American (AMR) AF: 0.416 AC: 6347 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1681 AN: 5146

South Asian (SAS) AF: 0.516 AC: 2485 AN: 4820

European-Finnish (FIN) AF: 0.333 AC: 3526 AN: 10578

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28175 AN: 67966

Other (OTH) AF: 0.481 AC: 1017 AN: 2114

Alfa AF: 0.440 Hom.: 29445

Bravo AF: 0.513

Asia WGS AF: 0.454 AC: 1583 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.47
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1349282; hg19: chr3-22648091;