17-4643264-A-G

Position:

• chr17-4643264-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 0.706 in 151,988 control chromosomes in the GnomAD database, including 39,336 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 0.71 (39336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107283 AN: 151870 Hom.: 39314 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.706 AC: 107340 AN: 151988 Hom.: 39336 Cov.: 31 AF XY: 0.716 AC XY: 53200 AN XY: 74308

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.721

Alfa AF: 0.730 Hom.: 5109

Bravo AF: 0.694

Asia WGS AF: 0.917 AC: 3186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9894225; hg19: chr17-4546559;