1-20092847-G-T

Variant names:

• chr1-20092847-G-T
• rs622450

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 0.904 in 152,316 control chromosomes in the GnomAD database, including 62,400 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 (62400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.904 AC: 137516 AN: 152198 Hom.: 62337 Cov.: 33

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.904 AC: 137638 AN: 152316 Hom.: 62400 Cov.: 33 AF XY: 0.905 AC XY: 67374 AN XY: 74480

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.909

Alfa AF: 0.870 Hom.: 25819

Bravo AF: 0.910

Asia WGS AF: 0.976 AC: 3392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs622450; hg19: chr1-20419340;