14-92285856-A-G

Variant names:

• chr14-92285856-A-G
• rs2025074

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 0.745 in 152,080 control chromosomes in the GnomAD database, including 42,626 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 0.74 (42626 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.745 AC: 113204 AN: 151962 Hom.: 42607 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.745 AC: 113272 AN: 152080 Hom.: 42626 Cov.: 31 AF XY: 0.747 AC XY: 55544 AN XY: 74352

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.768

Alfa AF: 0.766 Hom.: 60270

Bravo AF: 0.744

Asia WGS AF: 0.842 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.044
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025074; hg19: chr14-92752200;