21-28914008-G-C

Variant names:

• chr21-28914008-G-C
• rs11910981

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 0.2 in 152,040 control chromosomes in the GnomAD database, including 3,147 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 0.20 (3147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.200 AC: 30361 AN: 151922 Hom.: 3144 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.200 AC: 30382 AN: 152040 Hom.: 3147 Cov.: 32 AF XY: 0.202 AC XY: 14993 AN XY: 74320

African (AFR) AF: 0.241 AC: 10008 AN: 41462

American (AMR) AF: 0.163 AC: 2490 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3472

East Asian (EAS) AF: 0.101 AC: 524 AN: 5168

South Asian (SAS) AF: 0.237 AC: 1139 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2291 AN: 10552

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12654 AN: 67984

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.116 Hom.: 181

Bravo AF: 0.192

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs11910981; hg19: chr21-30286330;