20-4372091-T-C

Variant names:

• chr20-4372091-T-C
• rs6116326

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 0.198 in 152,102 control chromosomes in the GnomAD database, including 3,193 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 0.20 (3193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.198 AC: 30076 AN: 151984 Hom.: 3196 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.198 AC: 30075 AN: 152102 Hom.: 3193 Cov.: 32 AF XY: 0.193 AC XY: 14332 AN XY: 74374

African (AFR) AF: 0.141 AC: 5860 AN: 41476

American (AMR) AF: 0.233 AC: 3555 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3464

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5170

South Asian (SAS) AF: 0.133 AC: 640 AN: 4820

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15855 AN: 67970

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.218 Hom.: 2093

Bravo AF: 0.206

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.8
DANN	Benign	0.56
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs6116326; hg19: chr20-4352738;