rs11717333

Variant names:

• chr3-127100319-A-G
• rs11717333

Your query was ambiguous. Multiple possible variants found:

• chr3-127100319-A-G
• chr3-127100319-A-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 0.44 in 152,064 control chromosomes in the GnomAD database, including 15,020 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 0.44 (15020 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66907 AN: 151946 Hom.: 15016 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.440 AC: 66952 AN: 152064 Hom.: 15020 Cov.: 33 AF XY: 0.446 AC XY: 33119 AN XY: 74320

African (AFR) AF: 0.497 AC: 20622 AN: 41482

American (AMR) AF: 0.326 AC: 4975 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3464

East Asian (EAS) AF: 0.556 AC: 2864 AN: 5152

South Asian (SAS) AF: 0.540 AC: 2605 AN: 4822

European-Finnish (FIN) AF: 0.505 AC: 5333 AN: 10564

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27864 AN: 67988

Other (OTH) AF: 0.414 AC: 873 AN: 2110

Alfa AF: 0.420 Hom.: 8036

Bravo AF: 0.426

Asia WGS AF: 0.569 AC: 1976 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	1.4
DANN	Benign	0.82
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs11717333; hg19: chr3-126819162; COSMIC: COSV60111107;