rs1006899

Variant names:

• chr21-14472731-A-G
• rs1006899

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 0.171 in 151,320 control chromosomes in the GnomAD database, including 2,286 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 0.17 (2286 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 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: 0.171 AC: 25807 AN: 151202 Hom.: 2281 Cov.: 30

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.171 AC: 25835 AN: 151320 Hom.: 2286 Cov.: 30 AF XY: 0.170 AC XY: 12581 AN XY: 73900

African (AFR) AF: 0.209 AC: 8611 AN: 41144

American (AMR) AF: 0.115 AC: 1738 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 668 AN: 3472

East Asian (EAS) AF: 0.0469 AC: 241 AN: 5142

South Asian (SAS) AF: 0.233 AC: 1117 AN: 4788

European-Finnish (FIN) AF: 0.159 AC: 1660 AN: 10462

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11268 AN: 67864

Other (OTH) AF: 0.162 AC: 340 AN: 2098

Alfa AF: 0.165 Hom.: 8810

Bravo AF: 0.165

Asia WGS AF: 0.148 AC: 515 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1006899; hg19: chr21-15845052;