chr14-97859009-A-G

Variant names:

• chr14-97859009-A-G
• rs2615453

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 0.84 in 151,484 control chromosomes in the GnomAD database, including 53,703 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 0.84 (53703 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127091 AN: 151370 Hom.: 53655 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.840 AC: 127195 AN: 151484 Hom.: 53703 Cov.: 30 AF XY: 0.843 AC XY: 62390 AN XY: 74018

African (AFR) AF: 0.919 AC: 38024 AN: 41360

American (AMR) AF: 0.826 AC: 12560 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2842 AN: 3464

East Asian (EAS) AF: 0.833 AC: 4290 AN: 5150

South Asian (SAS) AF: 0.889 AC: 4273 AN: 4804

European-Finnish (FIN) AF: 0.853 AC: 8875 AN: 10402

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.790 AC: 53580 AN: 67784

Other (OTH) AF: 0.846 AC: 1786 AN: 2110

Alfa AF: 0.809 Hom.: 85531

Bravo AF: 0.838

Asia WGS AF: 0.856 AC: 2949 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2615453; hg19: chr14-98325346;