rs11137379

Variant names:

• chr9-138133487-G-A
• rs11137379

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 0.169 in 150,858 control chromosomes in the GnomAD database, including 3,339 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 0.17 (3339 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 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: 0.169 AC: 25434 AN: 150740 Hom.: 3339 Cov.: 31

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.169 AC: 25424 AN: 150858 Hom.: 3339 Cov.: 31 AF XY: 0.163 AC XY: 12027 AN XY: 73726

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.209

Alfa AF: 0.227 Hom.: 3686

Bravo AF: 0.170

Asia WGS AF: 0.0490 AC: 172 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11137379; hg19: chr9-141027939;