rs2094470

Variant names:

• chr1-55031629-C-T
• rs2094470

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.731 AC: 30310 AN: 41462

American (AMR) AF: 0.864 AC: 13205 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3222 AN: 3470

East Asian (EAS) AF: 0.926 AC: 4793 AN: 5174

South Asian (SAS) AF: 0.959 AC: 4616 AN: 4814

European-Finnish (FIN) AF: 0.914 AC: 9678 AN: 10592

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62898 AN: 68008

Other (OTH) AF: 0.891 AC: 1883 AN: 2114

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2094470; hg19: chr1-55497302;