11-113668358-A-G

Variant names:

• chr11-113668358-A-G
• rs3934007
• XR_001748390.2:n.5178+12975T>C

Variant summary

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

The XR_001748390.2(LOC107984390):​n.5178+12975T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,996 control chromosomes in the GnomAD database, including 31,061 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 0.63 (31061 hom., cov: 32)
• Consequence: LOC107984390 XR_001748390.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 10 publications found

Genes affected

LOC107984390 (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 (AFR) allele frequency at 95% confidence interval = 0.748 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: 0.631 AC: 95892 AN: 151878 Hom.: 31002 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.632 AC: 96012 AN: 151996 Hom.: 31061 Cov.: 32 AF XY: 0.627 AC XY: 46579 AN XY: 74310

African (AFR) AF: 0.755 AC: 31297 AN: 41448

American (AMR) AF: 0.672 AC: 10268 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3466

East Asian (EAS) AF: 0.663 AC: 3421 AN: 5162

South Asian (SAS) AF: 0.515 AC: 2482 AN: 4822

European-Finnish (FIN) AF: 0.533 AC: 5631 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39238 AN: 67950

Other (OTH) AF: 0.608 AC: 1280 AN: 2104

Alfa AF: 0.596 Hom.: 91566

Bravo AF: 0.654

Asia WGS AF: 0.606 AC: 2107 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	1.3
DANN	Benign	0.36
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3934007;

hg19: chr11-113539080;