20-187379-T-C

Variant names:

• chr20-187379-T-C
• rs13036722

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 0.158 in 151,990 control chromosomes in the GnomAD database, including 2,404 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 0.16 (2404 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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: 0.158 AC: 23999 AN: 151872 Hom.: 2395 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00560

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.158 AC: 24043 AN: 151990 Hom.: 2404 Cov.: 32 AF XY: 0.154 AC XY: 11439 AN XY: 74304

African (AFR) AF: 0.285 AC: 11818 AN: 41426

American (AMR) AF: 0.109 AC: 1655 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.00561 AC: 29 AN: 5166

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4824

European-Finnish (FIN) AF: 0.0660 AC: 699 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8500 AN: 67966

Other (OTH) AF: 0.137 AC: 290 AN: 2110

Alfa AF: 0.141 Hom.: 2956

Bravo AF: 0.165

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.72
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs13036722; hg19: chr20-168020;