chr17-45317812-A-G

Position:

• chr17-45317812-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.774 in 151,028 control chromosomes in the GnomAD database, including 46,332 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 0.77 (46332 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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: 0.774 AC: 116835 AN: 150912 Hom.: 46270 Cov.: 25

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.774 AC: 116955 AN: 151028 Hom.: 46332 Cov.: 25 AF XY: 0.771 AC XY: 56842 AN XY: 73708

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.745

Alfa AF: 0.742 Hom.: 18706

Bravo AF: 0.772

Asia WGS AF: 0.630 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	0.73
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4792849; hg19: chr17-43395178;