rs17361668

Variant names:

• chr11-102849613-T-A
• rs17361668

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 0.0932 in 152,242 control chromosomes in the GnomAD database, including 939 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 0.093 (939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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: 0.0932 AC: 14184 AN: 152124 Hom.: 938 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.0932 AC: 14186 AN: 152242 Hom.: 939 Cov.: 32 AF XY: 0.0946 AC XY: 7041 AN XY: 74428

African (AFR) AF: 0.0226 AC: 939 AN: 41574

American (AMR) AF: 0.0709 AC: 1085 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3472

East Asian (EAS) AF: 0.0261 AC: 135 AN: 5182

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4826

European-Finnish (FIN) AF: 0.206 AC: 2175 AN: 10570

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8785 AN: 68008

Other (OTH) AF: 0.0896 AC: 189 AN: 2110

Alfa AF: 0.115 Hom.: 144

Bravo AF: 0.0799

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs17361668; hg19: chr11-102720344;