rs17266994

Variant names:

• chr13-22682905-A-T
• rs17266994

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 152,158 control chromosomes in the GnomAD database, including 4,307 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 (4307 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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: 0.219 AC: 33342 AN: 152040 Hom.: 4298 Cov.: 33

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.219 AC: 33348 AN: 152158 Hom.: 4307 Cov.: 33 AF XY: 0.215 AC XY: 16008 AN XY: 74390

African (AFR) AF: 0.0911 AC: 3783 AN: 41530

American (AMR) AF: 0.310 AC: 4736 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3468

East Asian (EAS) AF: 0.0507 AC: 263 AN: 5186

South Asian (SAS) AF: 0.186 AC: 897 AN: 4824

European-Finnish (FIN) AF: 0.220 AC: 2329 AN: 10568

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19230 AN: 67988

Other (OTH) AF: 0.231 AC: 488 AN: 2108

Alfa AF: 0.258 Hom.: 756

Bravo AF: 0.223

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.76
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs17266994; hg19: chr13-23257044;