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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0264 AC: 1097 AN: 41508

American (AMR) AF: 0.213 AC: 3253 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2231 AN: 5170

South Asian (SAS) AF: 0.146 AC: 702 AN: 4814

European-Finnish (FIN) AF: 0.0925 AC: 979 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0777 AC: 5282 AN: 67986

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.0879 Hom.: 1738

Bravo AF: 0.104

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.83
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6124878; hg19: chr20-45497723;