20-2191281-T-C

Variant names:

• chr20-2191281-T-C
• rs6082345

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 0.617 in 152,042 control chromosomes in the GnomAD database, including 29,181 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 0.62 (29181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 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: 0.617 AC: 93778 AN: 151924 Hom.: 29160 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.617 AC: 93843 AN: 152042 Hom.: 29181 Cov.: 32 AF XY: 0.620 AC XY: 46072 AN XY: 74324

African (AFR) AF: 0.588 AC: 24377 AN: 41444

American (AMR) AF: 0.629 AC: 9608 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1899 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3935 AN: 5176

South Asian (SAS) AF: 0.657 AC: 3168 AN: 4824

European-Finnish (FIN) AF: 0.631 AC: 6669 AN: 10568

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.620 AC: 42128 AN: 67962

Other (OTH) AF: 0.593 AC: 1254 AN: 2114

Alfa AF: 0.588 Hom.: 9474

Bravo AF: 0.612

Asia WGS AF: 0.704 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.87
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs6082345; hg19: chr20-2171927;