chr3-120298633-G-A

Variant names:

• chr3-120298633-G-A
• rs796825

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 0.7 in 151,950 control chromosomes in the GnomAD database, including 37,447 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 0.70 (37447 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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: 0.700 AC: 106238 AN: 151832 Hom.: 37388 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.700 AC: 106357 AN: 151950 Hom.: 37447 Cov.: 31 AF XY: 0.704 AC XY: 52287 AN XY: 74288

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.681

Alfa AF: 0.659 Hom.: 31325

Bravo AF: 0.706

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs796825; hg19: chr3-120017480;