1-20557323-C-T

Position:

• chr1-20557323-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 0.796 in 152,060 control chromosomes in the GnomAD database, including 48,515 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 0.80 (48515 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20557323C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120898 AN: 151942 Hom.: 48473 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.796 AC: 120993 AN: 152060 Hom.: 48515 Cov.: 31 AF XY: 0.799 AC XY: 59369 AN XY: 74316

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.817

Alfa AF: 0.824 Hom.: 65541

Bravo AF: 0.794

Asia WGS AF: 0.886 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs677214; hg19: chr1-20883816;