17-5746568-G-C

Position:

• chr17-5746568-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.227 in 151,970 control chromosomes in the GnomAD database, including 5,061 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 0.23 (5061 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34517 AN: 151852 Hom.: 5060 Cov.: 31

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.227 AC: 34521 AN: 151970 Hom.: 5061 Cov.: 31 AF XY: 0.227 AC XY: 16857 AN XY: 74256

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.234

Alfa AF: 0.283 Hom.: 876

Bravo AF: 0.210

Asia WGS AF: 0.124 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8065677; hg19: chr17-5649888;