rs6098782

Variant names:

• chr20-55783511-A-C
• rs6098782

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 0.397 in 152,016 control chromosomes in the GnomAD database, including 14,972 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 (14972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 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: 0.397 AC: 60312 AN: 151896 Hom.: 14934 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.397 AC: 60404 AN: 152016 Hom.: 14972 Cov.: 32 AF XY: 0.388 AC XY: 28861 AN XY: 74324

African (AFR) AF: 0.702 AC: 29134 AN: 41486

American (AMR) AF: 0.270 AC: 4116 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.0440 AC: 228 AN: 5176

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4824

European-Finnish (FIN) AF: 0.290 AC: 3059 AN: 10560

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20408 AN: 67940

Other (OTH) AF: 0.368 AC: 774 AN: 2104

Alfa AF: 0.325 Hom.: 14955

Bravo AF: 0.408

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.50
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6098782; hg19: chr20-54358567;