20-44315384-C-T

Variant names:

• chr20-44315384-C-T
• rs12625067

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 0.0504 in 151,522 control chromosomes in the GnomAD database, including 715 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 0.050 (715 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0503 AC: 7609 AN: 151404 Hom.: 705 Cov.: 31

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0494

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

GnomAD4 genome AF: 0.0504 AC: 7630 AN: 151522 Hom.: 715 Cov.: 31 AF XY: 0.0572 AC XY: 4230 AN XY: 74006

African (AFR) AF: 0.0135 AC: 558 AN: 41326

American (AMR) AF: 0.186 AC: 2829 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 39 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1616 AN: 5122

South Asian (SAS) AF: 0.188 AC: 899 AN: 4794

European-Finnish (FIN) AF: 0.0164 AC: 171 AN: 10446

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0203 AC: 1381 AN: 67882

Other (OTH) AF: 0.0512 AC: 108 AN: 2108

Alfa AF: 0.0142 Hom.: 11

Bravo AF: 0.0586

Asia WGS AF: 0.254 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs12625067; hg19: chr20-42944024;