rs9912168

Positions:

• chr17-4419999-A-G
• chr17-4419999-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 0.39 in 151,916 control chromosomes in the GnomAD database, including 12,373 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 0.39 (12373 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4419999A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59250 AN: 151798 Hom.: 12354 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.390 AC: 59322 AN: 151916 Hom.: 12373 Cov.: 31 AF XY: 0.390 AC XY: 28939 AN XY: 74228

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.382

Alfa AF: 0.348 Hom.: 12582

Bravo AF: 0.402

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9912168; hg19: chr17-4323294;