rs13044579

chr20-6793773-A-G

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 0.0465 in 152,328 control chromosomes in the GnomAD database, including 214 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 0.046 (214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.08 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7092 AN: 152210 Hom.: 215 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.0578

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0465 AC: 7082 AN: 152328 Hom.: 214 Cov.: 32 AF XY: 0.0459 AC XY: 3418 AN XY: 74500

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.0575

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.0264

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0548 Hom.: 66

Bravo AF: 0.0470

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.1
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13044579; hg19: chr20-6774420;