rs17633986

Variant names:

• chr21-33146269-C-T
• rs17633986

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 0.089 in 152,284 control chromosomes in the GnomAD database, including 752 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 0.089 (752 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13554 AN: 152166 Hom.: 750 Cov.: 33

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0890 AC: 13554 AN: 152284 Hom.: 752 Cov.: 33 AF XY: 0.0892 AC XY: 6640 AN XY: 74456

African (AFR) AF: 0.0308 AC: 1278 AN: 41560

American (AMR) AF: 0.107 AC: 1638 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.103 AC: 532 AN: 5190

South Asian (SAS) AF: 0.137 AC: 660 AN: 4834

European-Finnish (FIN) AF: 0.0979 AC: 1037 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7873 AN: 68022

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.0821 Hom.: 95

Bravo AF: 0.0845

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17633986; hg19: chr21-34518575;