chr14-99683121-A-G

Variant names:

• chr14-99683121-A-G
• rs3783320

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 0.679 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.490 AC: 20303 AN: 41452

American (AMR) AF: 0.688 AC: 10521 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3093 AN: 5146

South Asian (SAS) AF: 0.841 AC: 4058 AN: 4826

European-Finnish (FIN) AF: 0.748 AC: 7932 AN: 10598

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52253 AN: 67978

Other (OTH) AF: 0.680 AC: 1435 AN: 2110

Alfa AF: 0.727 Hom.: 54603

Bravo AF: 0.664

Asia WGS AF: 0.711 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.42
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs3783320; hg19: chr14-100149458;