rs446717

Variant names:

• chr3-41106266-G-A
• rs446717

Your query was ambiguous. Multiple possible variants found:

• chr3-41106266-G-A
• chr3-41106266-G-C
• chr3-41106266-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 0.411 in 151,870 control chromosomes in the GnomAD database, including 14,076 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 (14076 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 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: 0.411 AC: 62417 AN: 151752 Hom.: 14075 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.411 AC: 62436 AN: 151870 Hom.: 14076 Cov.: 33 AF XY: 0.420 AC XY: 31191 AN XY: 74238

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.425

Alfa AF: 0.448 Hom.: 17838

Bravo AF: 0.408

Asia WGS AF: 0.590 AC: 2046 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs446717; hg19: chr3-41147757;