rs17630638

chr11-93062046-C-T

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 0.219 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.219 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

Gnomad4 AFR AF: 0.0747

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.230

Alfa AF: 0.284 Hom.: 6572

Bravo AF: 0.203

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.18
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17630638; hg19: chr11-92795212;