chr20-46007337-C-T

Variant names:

• chr20-46007337-C-T
• rs3918242

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 0.137 in 151,998 control chromosomes in the GnomAD database, including 1,511 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 (1511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 726 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.137 AC: 20853 AN: 151880 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.137 AC: 20867 AN: 151998 Hom.: 1511 Cov.: 32 AF XY: 0.138 AC XY: 10246 AN XY: 74286

African (AFR) AF: 0.121 AC: 5003 AN: 41456

American (AMR) AF: 0.0894 AC: 1365 AN: 15270

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

East Asian (EAS) AF: 0.141 AC: 729 AN: 5162

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4812

European-Finnish (FIN) AF: 0.171 AC: 1800 AN: 10530

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

European-Non Finnish (NFE) AF: 0.146 AC: 9933 AN: 67980

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.172 Hom.: 478

Bravo AF: 0.128

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.56
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3918242; hg19: chr20-44635976;