rs6084875

Variant names:

• chr20-4762059-G-A
• rs6084875

Your query was ambiguous. Multiple possible variants found:

• chr20-4762059-G-A
• chr20-4762059-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 0.377 in 152,104 control chromosomes in the GnomAD database, including 10,955 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 0.38 (10955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 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: 0.377 AC: 57310 AN: 151986 Hom.: 10941 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.377 AC: 57362 AN: 152104 Hom.: 10955 Cov.: 33 AF XY: 0.378 AC XY: 28127 AN XY: 74352

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.374

Alfa AF: 0.368 Hom.: 10309

Bravo AF: 0.386

Asia WGS AF: 0.341 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6084875; hg19: chr20-4742705;