rs2886927

Variant names:

• chr4-73864514-T-A
• rs2886927

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 0.461 in 152,050 control chromosomes in the GnomAD database, including 19,667 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 0.46 (19667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.461 AC: 69997 AN: 151930 Hom.: 19606 Cov.: 33

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.461 AC: 70118 AN: 152050 Hom.: 19667 Cov.: 33 AF XY: 0.460 AC XY: 34231 AN XY: 74354

African (AFR) AF: 0.790 AC: 32767 AN: 41460

American (AMR) AF: 0.491 AC: 7502 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2127 AN: 5178

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3285 AN: 10580

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19887 AN: 67964

Other (OTH) AF: 0.464 AC: 978 AN: 2106

Alfa AF: 0.381 Hom.: 1724

Bravo AF: 0.491

Asia WGS AF: 0.406 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.39
DANN	Benign	0.65
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2886927; hg19: chr4-74730231;