20-46007096-T-A

Variant names:

• chr20-46007096-T-A
• rs3918241

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 0.138 in 152,200 control chromosomes in the GnomAD database, including 1,536 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 0.14 (1536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20991 AN: 152082 Hom.: 1535 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.138 AC: 21007 AN: 152200 Hom.: 1536 Cov.: 32 AF XY: 0.139 AC XY: 10318 AN XY: 74420

African (AFR) AF: 0.122 AC: 5082 AN: 41532

American (AMR) AF: 0.0893 AC: 1365 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3470

East Asian (EAS) AF: 0.142 AC: 737 AN: 5184

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4814

European-Finnish (FIN) AF: 0.170 AC: 1804 AN: 10582

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

European-Non Finnish (NFE) AF: 0.146 AC: 9942 AN: 68012

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.150 Hom.: 267

Bravo AF: 0.129

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.60
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs3918241; hg19: chr20-44635735;