20-6780865-C-T

Variant names:

• chr20-6780865-C-T
• rs6054512

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 0.703 in 152,048 control chromosomes in the GnomAD database, including 38,735 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 0.70 (38735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.703 AC: 106759 AN: 151928 Hom.: 38690 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.703 AC: 106849 AN: 152048 Hom.: 38735 Cov.: 32 AF XY: 0.696 AC XY: 51754 AN XY: 74308

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.708

Alfa AF: 0.698 Hom.: 6422

Bravo AF: 0.723

Asia WGS AF: 0.609 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054512; hg19: chr20-6761512;