rs11244079

Positions:

• chr9-133317691-G-A

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 0.0579 in 708,598 control chromosomes in the GnomAD database, including 1,749 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 0.047 (322 hom., cov: 32)
  • Exomes 𝑓: 0.061 (1427 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

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 = 0.0637 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7206 AN: 152190 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.00723

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0629

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0350

GnomAD4 exome AF: 0.0608 AC: 33831 AN: 556290 Hom.: 1427 AF XY: 0.0623 AC XY: 17987 AN XY: 288936

Gnomad4 AFR exome AF: 0.00868

Gnomad4 AMR exome AF: 0.0235

Gnomad4 ASJ exome AF: 0.0628

Gnomad4 EAS exome AF: 0.000435

Gnomad4 SAS exome AF: 0.0762

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.0599

Gnomad4 OTH exome AF: 0.0532

GnomAD4 genome AF: 0.0473 AC: 7209 AN: 152308 Hom.: 322 Cov.: 32 AF XY: 0.0500 AC XY: 3720 AN XY: 74462

Gnomad4 AFR AF: 0.00721

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0636

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0579 Hom.: 186

Bravo AF: 0.0344

Asia WGS AF: 0.0260 AC: 89 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	6.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11244079; hg19: chr9-136184526;