rs17703427

Positions:

• chr17-70235867-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 0.102 in 152,214 control chromosomes in the GnomAD database, including 1,041 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 0.10 (1041 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

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 (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.70235867A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15544 AN: 152096 Hom.: 1037 Cov.: 32

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.102 AC: 15545 AN: 152214 Hom.: 1041 Cov.: 32 AF XY: 0.105 AC XY: 7791 AN XY: 74414

Gnomad4 AFR AF: 0.0266

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.146

Alfa AF: 0.127 Hom.: 1748

Bravo AF: 0.0922

Asia WGS AF: 0.210 AC: 730 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	2.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17703427; hg19: chr17-68232008;