rs11028186

Variant names:

• chr11-3574519-A-G
• rs11028186

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 0.122 in 152,146 control chromosomes in the GnomAD database, including 1,413 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 0.12 (1413 hom., cov: 32)
• Consequence: LOC107987159 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

LOC107987159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987159		n.3574519A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255367	ENST00000527970.1	n.285+6408T>C		intron_variant	Intron 1 of 4	3
ENSG00000255367	ENST00000710269.1	n.40+6408T>C		intron_variant	Intron 1 of 3
ENSG00000255367	ENST00000717868.1	n.323+6408T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18580 AN: 152028 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.122 AC: 18588 AN: 152146 Hom.: 1413 Cov.: 32 AF XY: 0.119 AC XY: 8823 AN XY: 74392

African (AFR) AF: 0.0363 AC: 1505 AN: 41498

American (AMR) AF: 0.135 AC: 2057 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.0518 AC: 268 AN: 5174

South Asian (SAS) AF: 0.110 AC: 529 AN: 4822

European-Finnish (FIN) AF: 0.113 AC: 1200 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11952 AN: 67986

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.149 Hom.: 337

Bravo AF: 0.120

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.53
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11028186; hg19: chr11-3595749;