rs17633258

Variant names:

• chr11-109115147-C-G
• rs17633258

Your query was ambiguous. Multiple possible variants found:

• chr11-109115147-C-G
• chr11-109115147-C-T

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 0.0374 in 152,254 control chromosomes in the GnomAD database, including 142 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 0.037 (142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 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: 0.0375 AC: 5702 AN: 152136 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.00884

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0420

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0374 AC: 5701 AN: 152254 Hom.: 142 Cov.: 32 AF XY: 0.0397 AC XY: 2957 AN XY: 74436

African (AFR) AF: 0.00888 AC: 369 AN: 41548

American (AMR) AF: 0.0526 AC: 804 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.0230 AC: 119 AN: 5180

South Asian (SAS) AF: 0.117 AC: 566 AN: 4824

European-Finnish (FIN) AF: 0.0591 AC: 626 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0420 AC: 2857 AN: 68028

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.00998 Hom.: 7

Bravo AF: 0.0340

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17633258; hg19: chr11-108985874;