chr20-3039444-C-T

Position:

• chr20-3039444-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.173 in 152,242 control chromosomes in the GnomAD database, including 2,554 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 (2554 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26352 AN: 152124 Hom.: 2538 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.173 AC: 26399 AN: 152242 Hom.: 2554 Cov.: 33 AF XY: 0.179 AC XY: 13316 AN XY: 74436

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.170

Alfa AF: 0.169 Hom.: 3076

Bravo AF: 0.172

Asia WGS AF: 0.329 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296236; hg19: chr20-3020090;