rs11103429

Variant names:

• chr9-134614732-A-G
• rs11103429

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.171 AC: 7097 AN: 41530

American (AMR) AF: 0.0489 AC: 748 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.0437 AC: 227 AN: 5194

South Asian (SAS) AF: 0.0704 AC: 340 AN: 4832

European-Finnish (FIN) AF: 0.0953 AC: 1011 AN: 10604

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3859 AN: 68022

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0664 Hom.: 1234

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
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs11103429; hg19: chr9-137506578;