rs6124878

Variant names:

• chr20-46869084-G-A
• rs6124878

Your query was ambiguous. Multiple possible variants found:

• chr20-46869084-G-A
• chr20-46869084-G-C
• chr20-46869084-G-T

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 0.0928 in 152,110 control chromosomes in the GnomAD database, including 1,226 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 0.093 (1226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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 (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.0928 AC: 14100 AN: 151992 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.0265

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.0928 AC: 14113 AN: 152110 Hom.: 1226 Cov.: 32 AF XY: 0.0983 AC XY: 7309 AN XY: 74368

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.0678

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0866 Hom.: 832

Bravo AF: 0.104

Asia WGS AF: 0.276 AC: 957 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	0.20
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6124878; hg19: chr20-45497723;