rs11039798

chr11-48518671-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 0.0936 in 152,204 control chromosomes in the GnomAD database, including 886 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 0.094 (886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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 (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14257 AN: 152086 Hom.: 888 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0936 AC: 14248 AN: 152204 Hom.: 886 Cov.: 32 AF XY: 0.0960 AC XY: 7146 AN XY: 74412

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.0789

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.108 Hom.: 161

Bravo AF: 0.0884

Asia WGS AF: 0.119 AC: 411 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	2.0
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11039798; hg19: chr11-48540223;