chr3-46117225-G-A

Variant names:

• chr3-46117225-G-A
• rs9879257

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 0.17 in 152,106 control chromosomes in the GnomAD database, including 5,675 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 0.17 (5675 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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: 0.170 AC: 25857 AN: 151988 Hom.: 5657 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.170 AC: 25924 AN: 152106 Hom.: 5675 Cov.: 31 AF XY: 0.163 AC XY: 12124 AN XY: 74378

African (AFR) AF: 0.513 AC: 21237 AN: 41420

American (AMR) AF: 0.0742 AC: 1135 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0102 AC: 49 AN: 4824

European-Finnish (FIN) AF: 0.0441 AC: 468 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0392 AC: 2663 AN: 67998

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.0745 Hom.: 312

Bravo AF: 0.192

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.25
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9879257; hg19: chr3-46158717;