3-14304207-C-T

Variant names:

• chr3-14304207-C-T
• rs9883639

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 0.327 in 152,088 control chromosomes in the GnomAD database, including 9,539 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 0.33 (9539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.327 AC: 49635 AN: 151972 Hom.: 9521 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.327 AC: 49672 AN: 152088 Hom.: 9539 Cov.: 32 AF XY: 0.330 AC XY: 24530 AN XY: 74340

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.355

Alfa AF: 0.378 Hom.: 22789

Bravo AF: 0.330

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.048
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9883639; hg19: chr3-14345707;