rs11103429

Variant names:

• chr9-134614732-A-G
• rs11103429

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 0.0896 in 152,272 control chromosomes in the GnomAD database, including 841 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 0.090 (841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.0896 AC: 13634 AN: 152154 Hom.: 839 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.0953

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0896 AC: 13648 AN: 152272 Hom.: 841 Cov.: 33 AF XY: 0.0898 AC XY: 6686 AN XY: 74462

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.0437

Gnomad4 SAS AF: 0.0704

Gnomad4 FIN AF: 0.0953

Gnomad4 NFE AF: 0.0567

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0612 Hom.: 414

Bravo AF: 0.0872

Asia WGS AF: 0.0730 AC: 252 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11103429; hg19: chr9-137506578;