13-85306989-G-A

Variant names:

• chr13-85306989-G-A
• rs1873288

Variant summary

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

The variant allele was found at a frequency of 0.784 in 151,932 control chromosomes in the GnomAD database, including 47,117 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 0.78 (47117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.784 AC: 118992 AN: 151814 Hom.: 47078 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.784 AC: 119073 AN: 151932 Hom.: 47117 Cov.: 32 AF XY: 0.777 AC XY: 57694 AN XY: 74242

African (AFR) AF: 0.804 AC: 33288 AN: 41402

American (AMR) AF: 0.721 AC: 10995 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2996 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2822 AN: 5156

South Asian (SAS) AF: 0.850 AC: 4092 AN: 4814

European-Finnish (FIN) AF: 0.662 AC: 6977 AN: 10538

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55175 AN: 67982

Other (OTH) AF: 0.786 AC: 1657 AN: 2108

Alfa AF: 0.806 Hom.: 81886

Bravo AF: 0.782

Asia WGS AF: 0.732 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.097
DANN	Benign	0.18
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1873288; hg19: chr13-85881124;