chr20-6789641-C-T

Variant names:

• chr20-6789641-C-T
• rs6054514

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 0.13 in 152,126 control chromosomes in the GnomAD database, including 2,098 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 0.13 (2098 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.129 AC: 19674 AN: 152008 Hom.: 2094 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.00713

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.130 AC: 19720 AN: 152126 Hom.: 2098 Cov.: 33 AF XY: 0.127 AC XY: 9430 AN XY: 74374

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0673

Gnomad4 OTH AF: 0.117

Alfa AF: 0.100 Hom.: 354

Bravo AF: 0.136

Asia WGS AF: 0.0530 AC: 183 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	0.093
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054514; hg19: chr20-6770288;