21-39145849-A-G

Variant names:

• chr21-39145849-A-G
• rs8126528

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 0.892 in 152,200 control chromosomes in the GnomAD database, including 60,692 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 0.89 (60692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.957 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: 0.892 AC: 135650 AN: 152082 Hom.: 60642 Cov.: 31

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.898

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.892 AC: 135757 AN: 152200 Hom.: 60692 Cov.: 31 AF XY: 0.893 AC XY: 66429 AN XY: 74412

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.901

Alfa AF: 0.870 Hom.: 12859

Bravo AF: 0.896

Asia WGS AF: 0.881 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8126528; hg19: chr21-40517775;