XR_001754723.1:n.130-815G>A

Variant names:

• chr20-55853891-G-A
• rs11907114
• XR_001754723.1:n.130-815G>A

Variant summary

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

The XR_001754723.1(LOC105372678):​n.130-815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,966 control chromosomes in the GnomAD database, including 8,696 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 0.33 (8696 hom., cov: 32)
• Consequence: LOC105372678 XR_001754723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 5 publications found

Genes affected

LOC105372678 (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 (AFR) allele frequency at 95% confidence interval = 0.383 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: 0.332 AC: 50374 AN: 151848 Hom.: 8695 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.332 AC: 50399 AN: 151966 Hom.: 8696 Cov.: 32 AF XY: 0.332 AC XY: 24677 AN XY: 74272

African (AFR) AF: 0.388 AC: 16090 AN: 41424

American (AMR) AF: 0.254 AC: 3875 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5180

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4816

European-Finnish (FIN) AF: 0.343 AC: 3617 AN: 10552

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22264 AN: 67946

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.330 Hom.: 25600

Bravo AF: 0.325

Asia WGS AF: 0.227 AC: 785 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.33
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs11907114; hg19: chr20-54428947;