17-5746568-G-C

Variant names:

• chr17-5746568-G-C
• rs8065677

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;