20-2803626-T-G

Position:

• chr20-2803626-T-G

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 0.883 in 152,060 control chromosomes in the GnomAD database, including 59,416 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 0.88 (59416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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 = 0.975 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: 0.883 AC: 134223 AN: 151942 Hom.: 59365 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.883 AC: 134333 AN: 152060 Hom.: 59416 Cov.: 31 AF XY: 0.885 AC XY: 65748 AN XY: 74308

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.891

Alfa AF: 0.883 Hom.: 7369

Bravo AF: 0.886

Asia WGS AF: 0.951 AC: 3307 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	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs107130; hg19: chr20-2784272;