6-17709320-A-G

Position:

• chr6-17709320-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 0.772 in 152,148 control chromosomes in the GnomAD database, including 45,529 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 (45529 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17709320A>G		intergenic_region
NUP153-AS1	NR_134618.1	n.320-1469A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117360 AN: 152030 Hom.: 45480 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.772 AC: 117463 AN: 152148 Hom.: 45529 Cov.: 33 AF XY: 0.775 AC XY: 57629 AN XY: 74380

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.784

Alfa AF: 0.771 Hom.: 18219

Bravo AF: 0.770

Asia WGS AF: 0.871 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
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: rs2328136; hg19: chr6-17709551;