rs11039130

Variant names:

• chr11-47207765-C-T
• rs11039130

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 0.199 in 152,066 control chromosomes in the GnomAD database, including 3,906 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 0.20 (3906 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 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: 0.199 AC: 30207 AN: 151948 Hom.: 3905 Cov.: 31

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.199 AC: 30208 AN: 152066 Hom.: 3906 Cov.: 31 AF XY: 0.194 AC XY: 14447 AN XY: 74330

African (AFR) AF: 0.0499 AC: 2070 AN: 41504

American (AMR) AF: 0.190 AC: 2895 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3470

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5178

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2201 AN: 10572

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19988 AN: 67962

Other (OTH) AF: 0.228 AC: 481 AN: 2106

Alfa AF: 0.252 Hom.: 8528

Bravo AF: 0.190

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.64
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11039130; hg19: chr11-47229316;