rs6107853

Variant names:

• chr20-6629230-G-A
• rs6107853

Your query was ambiguous. Multiple possible variants found:

• chr20-6629230-G-A
• chr20-6629230-G-C

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 0.398 in 151,932 control chromosomes in the GnomAD database, including 13,530 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 0.40 (13530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.398 AC: 60398 AN: 151814 Hom.: 13511 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.398 AC: 60441 AN: 151932 Hom.: 13530 Cov.: 32 AF XY: 0.406 AC XY: 30103 AN XY: 74234

African (AFR) AF: 0.202 AC: 8374 AN: 41478

American (AMR) AF: 0.506 AC: 7707 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4231 AN: 5138

South Asian (SAS) AF: 0.362 AC: 1747 AN: 4822

European-Finnish (FIN) AF: 0.523 AC: 5522 AN: 10560

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30120 AN: 67912

Other (OTH) AF: 0.404 AC: 851 AN: 2108

Alfa AF: 0.427 Hom.: 41268

Bravo AF: 0.392

Asia WGS AF: 0.548 AC: 1906 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6107853; hg19: chr20-6609877;