21-30386788-A-G

Variant names:

• chr21-30386788-A-G
• rs2250904

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 0.726 in 152,066 control chromosomes in the GnomAD database, including 40,856 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 (40856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 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: 0.726 AC: 110346 AN: 151948 Hom.: 40798 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.726 AC: 110467 AN: 152066 Hom.: 40856 Cov.: 32 AF XY: 0.724 AC XY: 53840 AN XY: 74314

African (AFR) AF: 0.873 AC: 36237 AN: 41522

American (AMR) AF: 0.693 AC: 10598 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3695 AN: 5130

South Asian (SAS) AF: 0.712 AC: 3426 AN: 4812

European-Finnish (FIN) AF: 0.625 AC: 6611 AN: 10572

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45180 AN: 67956

Other (OTH) AF: 0.714 AC: 1510 AN: 2114

Alfa AF: 0.697 Hom.: 15439

Bravo AF: 0.736

Asia WGS AF: 0.731 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.78
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2250904; hg19: chr21-31759106;