rs1699667

Variant names:

• chr21-24122388-T-C
• rs1699667

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 0.103 in 152,210 control chromosomes in the GnomAD database, including 1,639 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 0.10 (1639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.103 AC: 15660 AN: 152092 Hom.: 1637 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.103 AC: 15679 AN: 152210 Hom.: 1639 Cov.: 33 AF XY: 0.102 AC XY: 7569 AN XY: 74432

African (AFR) AF: 0.265 AC: 10992 AN: 41498

American (AMR) AF: 0.0807 AC: 1235 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.145 AC: 749 AN: 5176

South Asian (SAS) AF: 0.0512 AC: 247 AN: 4822

European-Finnish (FIN) AF: 0.00754 AC: 80 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2101 AN: 68016

Other (OTH) AF: 0.0894 AC: 189 AN: 2114

Alfa AF: 0.0675 Hom.: 132

Bravo AF: 0.116

Asia WGS AF: 0.0880 AC: 304 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.83
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1699667; hg19: chr21-25494701;