chr11-3574519-A-G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527970.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255367	ENST00000527970.1	TSL:3	n.285+6408T>C		intron	N/A
	ENSG00000255367	ENST00000710269.1		n.40+6408T>C		intron	N/A
	ENSG00000255367	ENST00000717868.1		n.323+6408T>C		intron	N/A

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 v4.9

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;