chr20-6759670-C-T

Variant names:

• chr20-6759670-C-T
• rs6077060

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 0.153 in 152,106 control chromosomes in the GnomAD database, including 2,523 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 0.15 (2523 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23200 AN: 151988 Hom.: 2519 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0879

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.153 AC: 23229 AN: 152106 Hom.: 2523 Cov.: 32 AF XY: 0.153 AC XY: 11356 AN XY: 74364

African (AFR) AF: 0.298 AC: 12345 AN: 41440

American (AMR) AF: 0.120 AC: 1829 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.193 AC: 996 AN: 5170

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4824

European-Finnish (FIN) AF: 0.0985 AC: 1043 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0879 AC: 5976 AN: 68010

Other (OTH) AF: 0.151 AC: 320 AN: 2114

Alfa AF: 0.115 Hom.: 3744

Bravo AF: 0.161

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.60
DANN	Benign	0.53
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6077060; hg19: chr20-6740317;