20-5298689-G-C

Position:

• chr20-5298689-G-C

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 0.73 in 151,654 control chromosomes in the GnomAD database, including 40,411 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 0.73 (40411 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110655 AN: 151536 Hom.: 40368 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 110748 AN: 151654 Hom.: 40411 Cov.: 33 AF XY: 0.732 AC XY: 54226 AN XY: 74092

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.737

Alfa AF: 0.735 Hom.: 5110

Bravo AF: 0.727

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs927103; hg19: chr20-5279335;