XR_001748281.1:n.231-1966G>A

Variant names:

• chr11-68678956-C-T
• rs2187331
• XR_001748281.1:n.231-1966G>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.231-1966G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,116 control chromosomes in the GnomAD database, including 54,420 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 0.85 (54420 hom., cov: 31)
• Consequence: LOC107984343 XR_001748281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 22 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.845 AC: 128480 AN: 151998 Hom.: 54374 Cov.: 31

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.845 AC: 128587 AN: 152116 Hom.: 54420 Cov.: 31 AF XY: 0.849 AC XY: 63172 AN XY: 74368

African (AFR) AF: 0.881 AC: 36543 AN: 41484

American (AMR) AF: 0.815 AC: 12440 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3069 AN: 3468

East Asian (EAS) AF: 0.888 AC: 4589 AN: 5166

South Asian (SAS) AF: 0.861 AC: 4155 AN: 4826

European-Finnish (FIN) AF: 0.909 AC: 9616 AN: 10582

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55423 AN: 68004

Other (OTH) AF: 0.828 AC: 1746 AN: 2108

Alfa AF: 0.823 Hom.: 163866

Bravo AF: 0.836

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2187331; hg19: chr11-68446424;