chr17-47725508-A-G

Position:

• chr17-47725508-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 0.394 in 151,770 control chromosomes in the GnomAD database, including 12,177 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 0.39 (12177 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.457 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: 0.394 AC: 59817 AN: 151652 Hom.: 12175 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.394 AC: 59843 AN: 151770 Hom.: 12177 Cov.: 31 AF XY: 0.399 AC XY: 29591 AN XY: 74158

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.398

Alfa AF: 0.418 Hom.: 11229

Bravo AF: 0.387

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9910408; hg19: chr17-45802874; COSMIC: COSV55557543;