11-118694522-C-T

Variant names:

• chr11-118694522-C-T
• rs519982
• XR_007062909.1:n.251+1407C>T

Variant summary

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

The XR_948068.3(LOC105369519):​n.342+1407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,020 control chromosomes in the GnomAD database, including 8,108 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 0.32 (8108 hom., cov: 32)
• Consequence: LOC105369519 XR_948068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 11 publications found

Genes affected

LOC105369519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 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: 0.318 AC: 48352 AN: 151902 Hom.: 8094 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.318 AC: 48388 AN: 152020 Hom.: 8108 Cov.: 32 AF XY: 0.318 AC XY: 23662 AN XY: 74300

African (AFR) AF: 0.249 AC: 10336 AN: 41444

American (AMR) AF: 0.460 AC: 7012 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1258 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2092 AN: 5156

South Asian (SAS) AF: 0.189 AC: 912 AN: 4820

European-Finnish (FIN) AF: 0.313 AC: 3306 AN: 10578

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22222 AN: 67976

Other (OTH) AF: 0.335 AC: 707 AN: 2112

Alfa AF: 0.319 Hom.: 4054

Bravo AF: 0.334

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.68
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs519982; hg19: chr11-118565231;