14-85270825-A-G

Variant names:

• chr14-85270825-A-G
• rs1867082

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 0.566 in 151,912 control chromosomes in the GnomAD database, including 25,506 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 0.57 (25506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.69 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: 0.566 AC: 85934 AN: 151794 Hom.: 25483 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.566 AC: 86004 AN: 151912 Hom.: 25506 Cov.: 32 AF XY: 0.559 AC XY: 41496 AN XY: 74244

African (AFR) AF: 0.696 AC: 28850 AN: 41432

American (AMR) AF: 0.466 AC: 7089 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1921 AN: 3460

East Asian (EAS) AF: 0.0824 AC: 424 AN: 5146

South Asian (SAS) AF: 0.362 AC: 1749 AN: 4826

European-Finnish (FIN) AF: 0.584 AC: 6175 AN: 10574

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38062 AN: 67926

Other (OTH) AF: 0.529 AC: 1120 AN: 2116

Alfa AF: 0.556 Hom.: 75206

Bravo AF: 0.562

Asia WGS AF: 0.251 AC: 876 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	0.36
DANN	Benign	0.69
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1867082; hg19: chr14-85737169;