chr20-39280311-T-C

Position:

• chr20-39280311-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;