14-92285856-A-G

Variant names:

• chr14-92285856-A-G
• rs2025074

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 0.745 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.644 AC: 26676 AN: 41454

American (AMR) AF: 0.790 AC: 12076 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4800 AN: 5160

South Asian (SAS) AF: 0.840 AC: 4047 AN: 4820

European-Finnish (FIN) AF: 0.773 AC: 8182 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52168 AN: 67988

Other (OTH) AF: 0.768 AC: 1623 AN: 2112

Alfa AF: 0.765 Hom.: 83566

Bravo AF: 0.744

Asia WGS AF: 0.842 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.044
DANN	Benign	0.59
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2025074; hg19: chr14-92752200;