rs9909179

Variant names:

• chr17-13140986-T-C
• rs9909179

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 0.37 in 151,960 control chromosomes in the GnomAD database, including 10,645 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 0.37 (10645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

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 (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56188 AN: 151842 Hom.: 10632 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.370 AC: 56220 AN: 151960 Hom.: 10645 Cov.: 32 AF XY: 0.373 AC XY: 27702 AN XY: 74262

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.373

Alfa AF: 0.392 Hom.: 14083

Bravo AF: 0.356

Asia WGS AF: 0.463 AC: 1606 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	7.6
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9909179; hg19: chr17-13044303;