chr3-126976937-A-G

Position:

• chr3-126976937-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;