14-97859009-A-G

Variant names:

• chr14-97859009-A-G
• rs2615453

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 0.84 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.840 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

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.846

Alfa AF: 0.801 Hom.: 54997

Bravo AF: 0.838

Asia WGS AF: 0.856 AC: 2949 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2615453; hg19: chr14-98325346;