20-1425568-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 0.811 in 151,970 control chromosomes in the GnomAD database, including 49,974 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 0.81 (49974 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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: 0.811 AC: 123136 AN: 151850 Hom.: 49932 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.811 AC: 123242 AN: 151970 Hom.: 49974 Cov.: 30 AF XY: 0.806 AC XY: 59840 AN XY: 74260

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.795

Alfa AF: 0.800 Hom.: 66220

Bravo AF: 0.820

Asia WGS AF: 0.789 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6042209; hg19: chr20-1406212;