rs446717

chr3-41106266-G-Achr3-41106266-G-Cchr3-41106266-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/exons	MANE	UniProt

Ensembl

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