13-20293921-G-A

Variant names:

• chr13-20293921-G-A
• rs1547721

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 0.326 in 151,900 control chromosomes in the GnomAD database, including 9,067 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 (9067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 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: 0.326 AC: 49510 AN: 151782 Hom.: 9056 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.326 AC: 49564 AN: 151900 Hom.: 9067 Cov.: 31 AF XY: 0.328 AC XY: 24317 AN XY: 74228

African (AFR) AF: 0.170 AC: 7034 AN: 41438

American (AMR) AF: 0.287 AC: 4384 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2091 AN: 5170

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4306 AN: 10504

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27675 AN: 67906

Other (OTH) AF: 0.332 AC: 699 AN: 2108

Alfa AF: 0.382 Hom.: 7842

Bravo AF: 0.306

Asia WGS AF: 0.457 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.53
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1547721; hg19: chr13-20868060;