rs1006899

Variant names:

• chr21-14472731-A-G
• rs1006899

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.171 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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.162

Alfa AF: 0.163 Hom.: 3561

Bravo AF: 0.165

Asia WGS AF: 0.148 AC: 515 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1006899; hg19: chr21-15845052;