1-55022696-A-G

Position:

• chr1-55022696-A-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 0.705 in 152,208 control chromosomes in the GnomAD database, including 38,177 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 0.71 (38177 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55022696A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107301 AN: 152088 Hom.: 38171 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.705 AC: 107353 AN: 152208 Hom.: 38177 Cov.: 33 AF XY: 0.703 AC XY: 52324 AN XY: 74428

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.676

Alfa AF: 0.699 Hom.: 13263

Bravo AF: 0.689

Asia WGS AF: 0.606 AC: 2105 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	0.95
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2479393; hg19: chr1-55488369;