chr13-20300771-A-G

Variant names:

• chr13-20300771-A-G
• rs4769989
• XR_941720.2:n.106+4978A>G

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+4978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,006 control chromosomes in the GnomAD database, including 22,848 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 0.54 (22848 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 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: 0.545 AC: 82741 AN: 151888 Hom.: 22824 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.545 AC: 82812 AN: 152006 Hom.: 22848 Cov.: 32 AF XY: 0.539 AC XY: 40051 AN XY: 74300

African (AFR) AF: 0.545 AC: 22584 AN: 41426

American (AMR) AF: 0.531 AC: 8118 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1224 AN: 5174

South Asian (SAS) AF: 0.508 AC: 2446 AN: 4816

European-Finnish (FIN) AF: 0.529 AC: 5583 AN: 10558

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39216 AN: 67966

Other (OTH) AF: 0.538 AC: 1133 AN: 2104

Alfa AF: 0.564 Hom.: 77495

Bravo AF: 0.545

Asia WGS AF: 0.445 AC: 1548 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.98
DANN	Benign	0.81
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4769989; hg19: chr13-20874910;