21-39093586-G-T

Variant names:

• chr21-39093586-G-T
• rs4817986

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 0.225 in 152,236 control chromosomes in the GnomAD database, including 4,254 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 0.23 (4254 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.279 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: 0.225 AC: 34276 AN: 152116 Hom.: 4241 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.225 AC: 34309 AN: 152236 Hom.: 4254 Cov.: 33 AF XY: 0.226 AC XY: 16836 AN XY: 74422

African (AFR) AF: 0.128 AC: 5301 AN: 41566

American (AMR) AF: 0.286 AC: 4374 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3468

East Asian (EAS) AF: 0.169 AC: 875 AN: 5174

South Asian (SAS) AF: 0.250 AC: 1209 AN: 4828

European-Finnish (FIN) AF: 0.230 AC: 2430 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18357 AN: 68002

Other (OTH) AF: 0.233 AC: 491 AN: 2104

Alfa AF: 0.251 Hom.: 8281

Bravo AF: 0.228

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs4817986; hg19: chr21-40465512;