chr3-126976937-A-G

Variant names:

• chr3-126976937-A-G
• rs9822602

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.414 in 152,124 control chromosomes in the GnomAD database, including 14,738 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 0.41 (14738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62942 AN: 152006 Hom.: 14712 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.414 AC: 63017 AN: 152124 Hom.: 14738 Cov.: 33 AF XY: 0.412 AC XY: 30653 AN XY: 74360

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.396

Alfa AF: 0.367 Hom.: 1858

Bravo AF: 0.428

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9822602; hg19: chr3-126695780;