17-55390852-C-T

Variant names:

• chr17-55390852-C-T
• rs888206

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 0.491 in 152,038 control chromosomes in the GnomAD database, including 18,393 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 0.49 (18393 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• 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 (AFR) allele frequency at 95% confidence interval = 0.528 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: 0.491 AC: 74570 AN: 151920 Hom.: 18372 Cov.: 33

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.491 AC: 74628 AN: 152038 Hom.: 18393 Cov.: 33 AF XY: 0.489 AC XY: 36356 AN XY: 74334

African (AFR) AF: 0.534 AC: 22135 AN: 41472

American (AMR) AF: 0.472 AC: 7204 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2092 AN: 5168

South Asian (SAS) AF: 0.433 AC: 2089 AN: 4826

European-Finnish (FIN) AF: 0.447 AC: 4719 AN: 10552

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33390 AN: 67974

Other (OTH) AF: 0.463 AC: 978 AN: 2112

Alfa AF: 0.490 Hom.: 10280

Bravo AF: 0.497

Asia WGS AF: 0.446 AC: 1551 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	0.11
DANN	Benign	0.24
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs888206; hg19: chr17-53468213;