11-113637703-A-G

Variant names:

• chr11-113637703-A-G
• rs1022084
• XR_001748390.2:n.5178+43630T>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+43630T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,090 control chromosomes in the GnomAD database, including 16,611 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 0.46 (16611 hom., cov: 32)
• Consequence: LOC107984390 XR_001748390.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 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: 0.462 AC: 70252 AN: 151972 Hom.: 16574 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.463 AC: 70344 AN: 152090 Hom.: 16611 Cov.: 32 AF XY: 0.468 AC XY: 34765 AN XY: 74348

African (AFR) AF: 0.504 AC: 20916 AN: 41510

American (AMR) AF: 0.539 AC: 8234 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3470

East Asian (EAS) AF: 0.661 AC: 3406 AN: 5152

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4822

European-Finnish (FIN) AF: 0.457 AC: 4832 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28064 AN: 67984

Other (OTH) AF: 0.454 AC: 956 AN: 2104

Alfa AF: 0.344 Hom.: 1129

Bravo AF: 0.478

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.026
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1022084; hg19: chr11-113508425;