chr1-205755900-C-T

Variant names:

• chr1-205755900-C-T
• rs823122

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 0.832 in 152,140 control chromosomes in the GnomAD database, including 54,436 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 0.83 (54436 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126487 AN: 152024 Hom.: 54422 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.832 AC: 126551 AN: 152140 Hom.: 54436 Cov.: 31 AF XY: 0.832 AC XY: 61901 AN XY: 74388

African (AFR) AF: 0.588 AC: 24360 AN: 41438

American (AMR) AF: 0.859 AC: 13134 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3472

East Asian (EAS) AF: 0.855 AC: 4424 AN: 5172

South Asian (SAS) AF: 0.867 AC: 4177 AN: 4818

European-Finnish (FIN) AF: 0.957 AC: 10160 AN: 10616

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.946 AC: 64334 AN: 68018

Other (OTH) AF: 0.845 AC: 1779 AN: 2106

Alfa AF: 0.907 Hom.: 53639

Bravo AF: 0.811

Asia WGS AF: 0.844 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs823122; hg19: chr1-205725028;