rs17699436

Positions:

• chr17-47751209-A-G
• chr17-47751209-A-T

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 0.0748 in 151,838 control chromosomes in the GnomAD database, including 546 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 0.075 (546 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47751209A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11358 AN: 151718 Hom.: 544 Cov.: 31

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0748 AC: 11352 AN: 151838 Hom.: 546 Cov.: 31 AF XY: 0.0774 AC XY: 5747 AN XY: 74238

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0842 Hom.: 525

Bravo AF: 0.0719

Asia WGS AF: 0.136 AC: 477 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17699436; hg19: chr17-45828575;