rs6124878

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;