rs6107853

chr20-6629230-G-Achr20-6629230-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 0.398 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.404

Alfa AF: 0.430 Hom.: 14473

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6107853; hg19: chr20-6609877;