20-4406487-C-T

Position:

• chr20-4406487-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 0.902 in 152,214 control chromosomes in the GnomAD database, including 62,067 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 0.90 (62067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.902 AC: 137224 AN: 152096 Hom.: 62002 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.902 AC: 137349 AN: 152214 Hom.: 62067 Cov.: 31 AF XY: 0.905 AC XY: 67384 AN XY: 74426

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.879

Alfa AF: 0.879 Hom.: 4550

Bravo AF: 0.901

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs586446; hg19: chr20-4387134;