21-30827041-A-G

Variant names:

• chr21-30827041-A-G
• rs10154126

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 0.43 in 152,086 control chromosomes in the GnomAD database, including 14,435 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 0.43 (14435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65319 AN: 151966 Hom.: 14414 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.430 AC: 65384 AN: 152086 Hom.: 14435 Cov.: 32 AF XY: 0.432 AC XY: 32147 AN XY: 74336

African (AFR) AF: 0.364 AC: 15116 AN: 41498

American (AMR) AF: 0.560 AC: 8566 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3462

East Asian (EAS) AF: 0.446 AC: 2303 AN: 5164

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4818

European-Finnish (FIN) AF: 0.460 AC: 4862 AN: 10574

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29375 AN: 67958

Other (OTH) AF: 0.448 AC: 947 AN: 2112

Alfa AF: 0.431 Hom.: 1876

Bravo AF: 0.434

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs10154126; hg19: chr21-32199359;