rs17219926

chr9-114817573-T-C

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 0.407 in 151,958 control chromosomes in the GnomAD database, including 13,968 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 0.41 (13968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61805 AN: 151840 Hom.: 13968 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.407 AC: 61813 AN: 151958 Hom.: 13968 Cov.: 31 AF XY: 0.404 AC XY: 29989 AN XY: 74296

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.426

Alfa AF: 0.453 Hom.: 2097

Bravo AF: 0.388

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17219926; hg19: chr9-117579853;