rs17630638

Variant names:

• chr11-93062046-C-T
• rs17630638

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 0.219 in 152,114 control chromosomes in the GnomAD database, including 4,541 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 0.22 (4541 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.219 AC: 33278 AN: 151996 Hom.: 4543 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.219 AC: 33265 AN: 152114 Hom.: 4541 Cov.: 33 AF XY: 0.216 AC XY: 16053 AN XY: 74374

African (AFR) AF: 0.0747 AC: 3103 AN: 41520

American (AMR) AF: 0.198 AC: 3019 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3466

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5178

South Asian (SAS) AF: 0.166 AC: 799 AN: 4826

European-Finnish (FIN) AF: 0.314 AC: 3318 AN: 10552

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20936 AN: 67972

Other (OTH) AF: 0.230 AC: 487 AN: 2114

Alfa AF: 0.274 Hom.: 8082

Bravo AF: 0.203

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17630638; hg19: chr11-92795212;