13-20307007-G-A

Variant names:

• chr13-20307007-G-A
• rs1953516
• XR_941720.2:n.106+11214G>A

Variant summary

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

The XR_941720.2(LOC105370102):​n.106+11214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,096 control chromosomes in the GnomAD database, including 12,708 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 0.39 (12708 hom., cov: 33)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 3 publications found

Genes affected

LOC105370102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 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: 0.391 AC: 59487 AN: 151978 Hom.: 12705 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.391 AC: 59509 AN: 152096 Hom.: 12708 Cov.: 33 AF XY: 0.389 AC XY: 28932 AN XY: 74326

African (AFR) AF: 0.234 AC: 9693 AN: 41484

American (AMR) AF: 0.427 AC: 6526 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1149 AN: 5178

South Asian (SAS) AF: 0.404 AC: 1952 AN: 4826

European-Finnish (FIN) AF: 0.465 AC: 4902 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32723 AN: 67976

Other (OTH) AF: 0.381 AC: 804 AN: 2112

Alfa AF: 0.446 Hom.: 66924

Bravo AF: 0.380

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.75
PhyloP100		1.5

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: rs1953516;

hg19: chr13-20881146;