rs2094470

Positions:

• chr1-55031629-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 0.866 in 152,130 control chromosomes in the GnomAD database, including 57,604 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 0.87 (57604 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

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 (SAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131673 AN: 152012 Hom.: 57587 Cov.: 31

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.866 AC: 131740 AN: 152130 Hom.: 57604 Cov.: 31 AF XY: 0.867 AC XY: 64523 AN XY: 74382

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.891

Alfa AF: 0.872 Hom.: 9223

Bravo AF: 0.855

Asia WGS AF: 0.931 AC: 3238 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	0.74
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2094470; hg19: chr1-55497302;