chr21-39808149-A-G

Position:

• chr21-39808149-A-G

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 0.711 in 151,868 control chromosomes in the GnomAD database, including 40,030 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 0.71 (40030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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: 0.710 AC: 107809 AN: 151750 Hom.: 39966 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.711 AC: 107935 AN: 151868 Hom.: 40030 Cov.: 31 AF XY: 0.714 AC XY: 52995 AN XY: 74204

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.721

Alfa AF: 0.620 Hom.: 13406

Bravo AF: 0.731

Asia WGS AF: 0.865 AC: 3007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2410182; hg19: chr21-41180076;