11-68682735-C-T

Variant names:

• chr11-68682735-C-T
• rs948854
• XR_001748281.1:n.230+5106G>A

Variant summary

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

The XR_001748281.1(LOC107984343):​n.230+5106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,006 control chromosomes in the GnomAD database, including 34,922 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 0.66 (34922 hom., cov: 31)
• Consequence: LOC107984343 XR_001748281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 20 publications found

Genes affected

LOC107984343 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.661 AC: 100374 AN: 151888 Hom.: 34910 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.661 AC: 100412 AN: 152006 Hom.: 34922 Cov.: 31 AF XY: 0.672 AC XY: 49910 AN XY: 74298

African (AFR) AF: 0.430 AC: 17829 AN: 41422

American (AMR) AF: 0.710 AC: 10852 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2640 AN: 3470

East Asian (EAS) AF: 0.868 AC: 4484 AN: 5164

South Asian (SAS) AF: 0.786 AC: 3778 AN: 4808

European-Finnish (FIN) AF: 0.883 AC: 9357 AN: 10602

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49187 AN: 67952

Other (OTH) AF: 0.664 AC: 1402 AN: 2110

Alfa AF: 0.692 Hom.: 60480

Bravo AF: 0.634

Asia WGS AF: 0.802 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.069
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs948854; hg19: chr11-68450203;