chr20-211156-G-T

Variant names:

• chr20-211156-G-T
• rs6074578

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 0.388 in 152,016 control chromosomes in the GnomAD database, including 11,904 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 0.39 (11904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58940 AN: 151898 Hom.: 11907 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.388 AC: 58957 AN: 152016 Hom.: 11904 Cov.: 32 AF XY: 0.394 AC XY: 29288 AN XY: 74314

African (AFR) AF: 0.292 AC: 12117 AN: 41464

American (AMR) AF: 0.407 AC: 6223 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2735 AN: 5170

South Asian (SAS) AF: 0.505 AC: 2428 AN: 4812

European-Finnish (FIN) AF: 0.458 AC: 4852 AN: 10588

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28132 AN: 67924

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.397 Hom.: 39408

Bravo AF: 0.376

Asia WGS AF: 0.463 AC: 1607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.77
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6074578; hg19: chr20-191797;