17-54470764-A-G

Position:

• chr17-54470764-A-G

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 0.331 in 152,004 control chromosomes in the GnomAD database, including 11,410 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 0.33 (11410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.331 AC: 50204 AN: 151886 Hom.: 11383 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.331 AC: 50277 AN: 152004 Hom.: 11410 Cov.: 32 AF XY: 0.325 AC XY: 24107 AN XY: 74284

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0515

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.264

Alfa AF: 0.230 Hom.: 9418

Bravo AF: 0.342

Asia WGS AF: 0.140 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6504909; hg19: chr17-52548125;