3-141190219-T-C

Position:

• chr3-141190219-T-C

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 0.858 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

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 (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.858 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

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.836

Alfa AF: 0.844 Hom.: 62427

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9859339; hg19: chr3-140909061;