chr3-189552208-T-C

Variant names:

• chr3-189552208-T-C
• rs3966009

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 0.805 in 151,980 control chromosomes in the GnomAD database, including 49,969 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 0.80 (49969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 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: 0.805 AC: 122219 AN: 151862 Hom.: 49942 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.805 AC: 122297 AN: 151980 Hom.: 49969 Cov.: 32 AF XY: 0.808 AC XY: 60032 AN XY: 74294

African (AFR) AF: 0.649 AC: 26878 AN: 41438

American (AMR) AF: 0.871 AC: 13296 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2802 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4025 AN: 5182

South Asian (SAS) AF: 0.857 AC: 4132 AN: 4820

European-Finnish (FIN) AF: 0.861 AC: 9103 AN: 10572

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59268 AN: 67912

Other (OTH) AF: 0.824 AC: 1740 AN: 2112

Alfa AF: 0.824 Hom.: 6749

Bravo AF: 0.798

Asia WGS AF: 0.805 AC: 2793 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.66
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs3966009; hg19: chr3-189269997;