11-102859908-A-G

Variant names:

• chr11-102859908-A-G
• rs674546
• XR_007062868.1:n.1991+4125A>G

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1991+4125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,050 control chromosomes in the GnomAD database, including 4,460 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 0.23 (4460 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 12 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34873 AN: 151930 Hom.: 4454 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.229 AC: 34891 AN: 152050 Hom.: 4460 Cov.: 32 AF XY: 0.228 AC XY: 16949 AN XY: 74312

African (AFR) AF: 0.345 AC: 14321 AN: 41464

American (AMR) AF: 0.154 AC: 2352 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 858 AN: 3466

East Asian (EAS) AF: 0.136 AC: 701 AN: 5172

South Asian (SAS) AF: 0.174 AC: 837 AN: 4824

European-Finnish (FIN) AF: 0.247 AC: 2612 AN: 10566

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12445 AN: 67976

Other (OTH) AF: 0.220 AC: 465 AN: 2110

Alfa AF: 0.207 Hom.: 448

Bravo AF: 0.227

Asia WGS AF: 0.173 AC: 601 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.64
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs674546; hg19: chr11-102730639;