rs11186286

Variant names:

• chr10-90717319-T-C
• rs11186286
• XR_007062237.1:n.3373A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062237.1(LOC124902478):​n.3373A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,048 control chromosomes in the GnomAD database, including 3,768 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 (3768 hom., cov: 32)
• Consequence: LOC124902478 XR_007062237.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 3 publications found

Genes affected

LOC124902478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31039 AN: 151930 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.204 AC: 31074 AN: 152048 Hom.: 3768 Cov.: 32 AF XY: 0.198 AC XY: 14704 AN XY: 74338

African (AFR) AF: 0.334 AC: 13836 AN: 41428

American (AMR) AF: 0.160 AC: 2437 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0638 AC: 308 AN: 4824

European-Finnish (FIN) AF: 0.113 AC: 1194 AN: 10600

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12013 AN: 67966

Other (OTH) AF: 0.194 AC: 409 AN: 2110

Alfa AF: 0.185 Hom.: 8400

Bravo AF: 0.213

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs11186286; hg19: chr10-92477076;