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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.241 AC: 9993 AN: 41466

American (AMR) AF: 0.520 AC: 7948 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2000 AN: 3460

East Asian (EAS) AF: 0.634 AC: 3277 AN: 5168

South Asian (SAS) AF: 0.657 AC: 3160 AN: 4812

European-Finnish (FIN) AF: 0.418 AC: 4392 AN: 10510

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30167 AN: 67856

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.435 Hom.: 27691

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs446717; hg19: chr3-41147757;