rs796825

chr3-120298633-G-Achr3-120298633-G-Cchr3-120298633-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;