chr21-39820276-G-A

Variant names:

• chr21-39820276-G-A
• rs1984023

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 0.351 in 151,928 control chromosomes in the GnomAD database, including 9,721 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 0.35 (9721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53185 AN: 151810 Hom.: 9691 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.351 AC: 53264 AN: 151928 Hom.: 9721 Cov.: 32 AF XY: 0.354 AC XY: 26302 AN XY: 74216

African (AFR) AF: 0.382 AC: 15809 AN: 41438

American (AMR) AF: 0.456 AC: 6964 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2416 AN: 5150

South Asian (SAS) AF: 0.362 AC: 1742 AN: 4816

European-Finnish (FIN) AF: 0.301 AC: 3165 AN: 10532

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20709 AN: 67940

Other (OTH) AF: 0.339 AC: 716 AN: 2112

Alfa AF: 0.319 Hom.: 13654

Bravo AF: 0.366

Asia WGS AF: 0.404 AC: 1406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.57
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1984023; hg19: chr21-41192203;