chr20-6780865-C-T

Variant names:

• chr20-6780865-C-T
• rs6054512

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 0.703 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
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.703 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

African (AFR) AF: 0.886 AC: 36779 AN: 41520

American (AMR) AF: 0.683 AC: 10439 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2847 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3465 AN: 5156

South Asian (SAS) AF: 0.568 AC: 2728 AN: 4806

European-Finnish (FIN) AF: 0.574 AC: 6046 AN: 10542

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42262 AN: 67958

Other (OTH) AF: 0.708 AC: 1489 AN: 2104

Alfa AF: 0.687 Hom.: 12379

Bravo AF: 0.723

Asia WGS AF: 0.609 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.66
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6054512;

hg19: chr20-6761512;