chr20-45318510-C-T

Variant names:

• chr20-45318510-C-T
• rs2743345

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 0.173 in 152,078 control chromosomes in the GnomAD database, including 2,541 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 0.17 (2541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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: 0.173 AC: 26340 AN: 151960 Hom.: 2538 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.173 AC: 26358 AN: 152078 Hom.: 2541 Cov.: 32 AF XY: 0.174 AC XY: 12963 AN XY: 74320

African (AFR) AF: 0.118 AC: 4885 AN: 41474

American (AMR) AF: 0.146 AC: 2229 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.0183 AC: 95 AN: 5180

South Asian (SAS) AF: 0.151 AC: 726 AN: 4820

European-Finnish (FIN) AF: 0.245 AC: 2585 AN: 10554

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14444 AN: 67974

Other (OTH) AF: 0.181 AC: 382 AN: 2114

Alfa AF: 0.197 Hom.: 384

Bravo AF: 0.162

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.50
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2743345; hg19: chr20-43947150;