20-6603549-C-G

Variant names:

• chr20-6603549-C-G
• rs6107847

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 0.411 in 152,022 control chromosomes in the GnomAD database, including 13,394 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 0.41 (13394 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62369 AN: 151904 Hom.: 13374 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.411 AC: 62427 AN: 152022 Hom.: 13394 Cov.: 33 AF XY: 0.415 AC XY: 30868 AN XY: 74298

African (AFR) AF: 0.316 AC: 13092 AN: 41428

American (AMR) AF: 0.513 AC: 7837 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3753 AN: 5178

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4820

European-Finnish (FIN) AF: 0.462 AC: 4873 AN: 10552

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28486 AN: 67988

Other (OTH) AF: 0.427 AC: 903 AN: 2116

Alfa AF: 0.270 Hom.: 667

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.56
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs6107847; hg19: chr20-6584196;