rs6078524

Variant names:

• chr20-12339507-C-A
• rs6078524

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 0.277 in 151,986 control chromosomes in the GnomAD database, including 6,091 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 0.28 (6091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 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: 0.277 AC: 42057 AN: 151868 Hom.: 6086 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.277 AC: 42078 AN: 151986 Hom.: 6091 Cov.: 32 AF XY: 0.271 AC XY: 20157 AN XY: 74298

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.00657

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.272

Alfa AF: 0.299 Hom.: 1962

Bravo AF: 0.272

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
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: rs6078524; hg19: chr20-12320155;