chr21-39093586-G-T

Position:

• chr21-39093586-G-T

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 0.225 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.233

Alfa AF: 0.232 Hom.: 656

Bravo AF: 0.228

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4817986; hg19: chr21-40465512;