13-20207740-A-G

Variant names:

• chr13-20207740-A-G
• rs870729

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.678 in 151,824 control chromosomes in the GnomAD database, including 37,866 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 0.68 (37866 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102853 AN: 151706 Hom.: 37865 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.678 AC: 102883 AN: 151824 Hom.: 37866 Cov.: 31 AF XY: 0.681 AC XY: 50505 AN XY: 74202

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.679

Alfa AF: 0.798 Hom.: 51089

Bravo AF: 0.642

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870729; hg19: chr13-20781879;