chr17-22209747-C-T

Variant names:

• chr17-22209747-C-T
• rs17052370

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 0.183 in 151,980 control chromosomes in the GnomAD database, including 3,044 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 0.18 (3044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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: 0.184 AC: 27868 AN: 151860 Hom.: 3037 Cov.: 32

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.183 AC: 27888 AN: 151980 Hom.: 3044 Cov.: 32 AF XY: 0.183 AC XY: 13593 AN XY: 74278

African (AFR) AF: 0.0705 AC: 2925 AN: 41498

American (AMR) AF: 0.161 AC: 2459 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3470

East Asian (EAS) AF: 0.128 AC: 658 AN: 5150

South Asian (SAS) AF: 0.284 AC: 1367 AN: 4810

European-Finnish (FIN) AF: 0.232 AC: 2446 AN: 10560

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16008 AN: 67954

Other (OTH) AF: 0.230 AC: 484 AN: 2106

Alfa AF: 0.220 Hom.: 12962

Bravo AF: 0.171

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs17052370; hg19: chr17-21736353;