3-141190219-T-C

Variant names:

• chr3-141190219-T-C
• rs9859339

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 0.858 in 152,184 control chromosomes in the GnomAD database, including 56,079 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 0.86 (56079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.858 AC: 130408 AN: 152066 Hom.: 56036 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.858 AC: 130507 AN: 152184 Hom.: 56079 Cov.: 32 AF XY: 0.858 AC XY: 63846 AN XY: 74412

African (AFR) AF: 0.886 AC: 36766 AN: 41502

American (AMR) AF: 0.850 AC: 13004 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2880 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4801 AN: 5178

South Asian (SAS) AF: 0.925 AC: 4461 AN: 4824

European-Finnish (FIN) AF: 0.823 AC: 8726 AN: 10604

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57149 AN: 67996

Other (OTH) AF: 0.836 AC: 1765 AN: 2112

Alfa AF: 0.844 Hom.: 81525

Bravo AF: 0.857

Asia WGS AF: 0.907 AC: 3156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.33
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs9859339; hg19: chr3-140909061;