chr3-41106278-G-T

Variant names:

• chr3-41106278-G-T
• rs440640

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 151,840 control chromosomes in the GnomAD database, including 14,032 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 (14032 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62366 AN: 151722 Hom.: 14031 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.411 AC: 62385 AN: 151840 Hom.: 14032 Cov.: 33 AF XY: 0.420 AC XY: 31161 AN XY: 74224

African (AFR) AF: 0.241 AC: 10011 AN: 41470

American (AMR) AF: 0.520 AC: 7946 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2001 AN: 3462

East Asian (EAS) AF: 0.633 AC: 3274 AN: 5172

South Asian (SAS) AF: 0.646 AC: 3112 AN: 4820

European-Finnish (FIN) AF: 0.418 AC: 4382 AN: 10482

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

European-Non Finnish (NFE) AF: 0.445 AC: 30159 AN: 67840

Other (OTH) AF: 0.426 AC: 899 AN: 2110

Alfa AF: 0.300 Hom.: 777

Bravo AF: 0.408

Asia WGS AF: 0.585 AC: 2030 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs440640; hg19: chr3-41147769;