rs11103399

Variant names:

• chr9-134577961-A-G
• rs11103399

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 0.0707 in 152,314 control chromosomes in the GnomAD database, including 432 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 0.071 (432 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0936 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: 0.0707 AC: 10758 AN: 152196 Hom.: 432 Cov.: 33

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0707 AC: 10768 AN: 152314 Hom.: 432 Cov.: 33 AF XY: 0.0719 AC XY: 5357 AN XY: 74470

African (AFR) AF: 0.0961 AC: 3995 AN: 41572

American (AMR) AF: 0.0550 AC: 841 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5190

South Asian (SAS) AF: 0.0576 AC: 278 AN: 4830

European-Finnish (FIN) AF: 0.0900 AC: 955 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0632 AC: 4296 AN: 68018

Other (OTH) AF: 0.0506 AC: 107 AN: 2116

Alfa AF: 0.0637 Hom.: 61

Bravo AF: 0.0689

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.71
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs11103399; hg19: chr9-137469807;