3-41064574-A-G

Variant names:

• chr3-41064574-A-G
• rs429988

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 0.626 in 151,978 control chromosomes in the GnomAD database, including 30,107 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 0.63 (30107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95024 AN: 151860 Hom.: 30069 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.626 AC: 95108 AN: 151978 Hom.: 30107 Cov.: 32 AF XY: 0.616 AC XY: 45777 AN XY: 74292

African (AFR) AF: 0.611 AC: 25328 AN: 41430

American (AMR) AF: 0.543 AC: 8291 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3468

East Asian (EAS) AF: 0.465 AC: 2401 AN: 5160

South Asian (SAS) AF: 0.542 AC: 2606 AN: 4812

European-Finnish (FIN) AF: 0.589 AC: 6225 AN: 10564

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45871 AN: 67960

Other (OTH) AF: 0.620 AC: 1305 AN: 2106

Alfa AF: 0.650 Hom.: 17806

Bravo AF: 0.624

Asia WGS AF: 0.519 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.80
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs429988; hg19: chr3-41106065;