chr17-16973769-A-G

Position:

• chr17-16973769-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 0.86 in 152,314 control chromosomes in the GnomAD database, including 56,783 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 0.86 (56783 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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
		n.16973769A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130923 AN: 152194 Hom.: 56725 Cov.: 34

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.860 AC: 131041 AN: 152314 Hom.: 56783 Cov.: 34 AF XY: 0.862 AC XY: 64173 AN XY: 74476

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.840

Alfa AF: 0.819 Hom.: 48747

Bravo AF: 0.869

Asia WGS AF: 0.946 AC: 3290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7504096; hg19: chr17-16877083;