14-99683121-A-G

Variant names:

• chr14-99683121-A-G
• rs3783320

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 0.679 in 152,084 control chromosomes in the GnomAD database, including 36,267 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 0.68 (36267 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 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: 0.679 AC: 103158 AN: 151968 Hom.: 36266 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.679 AC: 103199 AN: 152084 Hom.: 36267 Cov.: 33 AF XY: 0.681 AC XY: 50649 AN XY: 74344

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.680

Alfa AF: 0.680 Hom.: 5830

Bravo AF: 0.664

Asia WGS AF: 0.711 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3783320; hg19: chr14-100149458;