21-30013925-G-A

Variant names:

• chr21-30013925-G-A
• rs9305406

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 0.735 in 151,896 control chromosomes in the GnomAD database, including 41,936 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 0.73 (41936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111517 AN: 151778 Hom.: 41910 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.735 AC: 111593 AN: 151896 Hom.: 41936 Cov.: 32 AF XY: 0.729 AC XY: 54143 AN XY: 74248

African (AFR) AF: 0.634 AC: 26297 AN: 41454

American (AMR) AF: 0.647 AC: 9858 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2822 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2595 AN: 5168

South Asian (SAS) AF: 0.592 AC: 2848 AN: 4810

European-Finnish (FIN) AF: 0.812 AC: 8562 AN: 10544

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 55993 AN: 67896

Other (OTH) AF: 0.745 AC: 1572 AN: 2110

Alfa AF: 0.783 Hom.: 119409

Bravo AF: 0.716

Asia WGS AF: 0.557 AC: 1937 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs9305406; hg19: chr21-31386243;