rs1006899

chr21-14472731-A-GchrNW_003315967.2-61176-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;