11-118604383-A-G

Variant names:

• chr11-118604383-A-G
• rs604096
• XR_007062908.1:n.3195T>C

Variant summary

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

The XR_007062908.1(LOC124902765):​n.3195T>C 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 0.249 in 152,110 control chromosomes in the GnomAD database, including 4,840 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 0.25 (4840 hom., cov: 32)
• Consequence: LOC124902765 XR_007062908.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 8 publications found

Genes affected

LOC124902765 (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 (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.249 AC: 37810 AN: 151992 Hom.: 4840 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.249 AC: 37832 AN: 152110 Hom.: 4840 Cov.: 32 AF XY: 0.252 AC XY: 18717 AN XY: 74384

African (AFR) AF: 0.276 AC: 11465 AN: 41486

American (AMR) AF: 0.179 AC: 2730 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1738 AN: 5176

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4822

European-Finnish (FIN) AF: 0.263 AC: 2780 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15859 AN: 67980

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.232 Hom.: 5816

Bravo AF: 0.240

Asia WGS AF: 0.367 AC: 1279 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	0.94
DANN	Benign	0.47
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs604096; hg19: chr11-118475098;