20-39280311-T-C

Variant names:

• chr20-39280311-T-C
• rs2208139

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 0.364 in 146,612 control chromosomes in the GnomAD database, including 10,833 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 0.36 (10833 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 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: 0.364 AC: 53347 AN: 146542 Hom.: 10824 Cov.: 26

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.364 AC: 53350 AN: 146612 Hom.: 10833 Cov.: 26 AF XY: 0.369 AC XY: 26369 AN XY: 71388

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.378

Alfa AF: 0.402 Hom.: 2173

Bravo AF: 0.366

Asia WGS AF: 0.526 AC: 1813 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	16
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2208139; hg19: chr20-37908954;