1-218686726-C-T

Variant names:

• chr1-218686726-C-T
• rs993925

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 0.327 in 152,014 control chromosomes in the GnomAD database, including 8,352 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 0.33 (8352 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 43 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 (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49692 AN: 151890 Hom.: 8346 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.327 AC: 49725 AN: 152014 Hom.: 8352 Cov.: 33 AF XY: 0.324 AC XY: 24100 AN XY: 74302

African (AFR) AF: 0.326 AC: 13537 AN: 41482

American (AMR) AF: 0.302 AC: 4611 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2556 AN: 5152

South Asian (SAS) AF: 0.295 AC: 1417 AN: 4800

European-Finnish (FIN) AF: 0.295 AC: 3112 AN: 10550

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22655 AN: 67964

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.334 Hom.: 34985

Bravo AF: 0.330

Asia WGS AF: 0.388 AC: 1351 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	5.7
DANN	Benign	0.24
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs993925; hg19: chr1-218860068; COSMIC: COSV107160408;