20-34150806-C-T

Variant names:

• chr20-34150806-C-T
• rs1015362

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 0.407 in 152,118 control chromosomes in the GnomAD database, including 15,859 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 0.41 (15859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.407 AC: 61889 AN: 152000 Hom.: 15832 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.407 AC: 61966 AN: 152118 Hom.: 15859 Cov.: 32 AF XY: 0.399 AC XY: 29690 AN XY: 74386

African (AFR) AF: 0.733 AC: 30395 AN: 41476

American (AMR) AF: 0.365 AC: 5573 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3470

East Asian (EAS) AF: 0.177 AC: 915 AN: 5182

South Asian (SAS) AF: 0.159 AC: 765 AN: 4824

European-Finnish (FIN) AF: 0.253 AC: 2677 AN: 10582

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19368 AN: 67982

Other (OTH) AF: 0.391 AC: 825 AN: 2112

Alfa AF: 0.314 Hom.: 33747

Bravo AF: 0.432

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.32
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1015362; hg19: chr20-32738612;